From 0e616329f571bacf53f6293d913d9e5c5e5f2748 Mon Sep 17 00:00:00 2001 From: Haibao Tang Date: Mon, 22 Jul 2024 10:03:09 +0800 Subject: [PATCH] Do not keep empty blocks (#690, thanks @Tong-Chen) (#692) * debug bp seq * Do not keep empty blocks (#690, thanks @Tong-Chen) * Add test_empty_blocks * move filter_blocks outside print_to_file --- jcvi/compara/base.py | 54 +- jcvi/compara/synteny.py | 6 +- jcvi/formats/maf.py | 14 +- .../synteny.py/inputs/test_empty_blocks.a.bed | 12 + .../inputs/test_empty_blocks.anchors | 19 + .../synteny.py/inputs/test_empty_blocks.b.bed | 13 + .../synteny.py/inputs/test_empty_blocks.last | 545 ++++++++++++++++++ .../test_empty_blocks.lifted.anchors | 16 + tests/compara/synteny.py/tests.yml | 7 + 9 files changed, 665 insertions(+), 21 deletions(-) create mode 100644 tests/compara/synteny.py/inputs/test_empty_blocks.a.bed create mode 100644 tests/compara/synteny.py/inputs/test_empty_blocks.anchors create mode 100644 tests/compara/synteny.py/inputs/test_empty_blocks.b.bed create mode 100644 tests/compara/synteny.py/inputs/test_empty_blocks.last create mode 100644 tests/compara/synteny.py/references/test_empty_blocks.lifted.anchors diff --git a/jcvi/compara/base.py b/jcvi/compara/base.py index 6cec765a..972a6ad3 100644 --- a/jcvi/compara/base.py +++ b/jcvi/compara/base.py @@ -1,4 +1,5 @@ from collections import defaultdict +from typing import Dict, Tuple from ..apps.base import logger from ..formats.base import BaseFile, read_block, must_open @@ -48,29 +49,52 @@ def make_ranges(self, order, clip=10): ranges.append(r) return ranges, block_pairs - def print_to_file(self, filename="stdout", accepted=None): - fw = must_open(filename, "w") - blocks = self.blocks + def filter_blocks(self, accepted: Dict[Tuple[str, str], str]): + """ + Filter the blocks based on the accepted pairs. This is used to update + the anchors so that they match the info in the LAST file. + """ + new_blocks = [] nremoved = 0 ncorrected = 0 - for block in blocks: - print("###", file=fw) + nblocks_removed = 0 + for block in self.blocks: + new_block = [] for line in block: a, b, score = line pair = (a, b) - if accepted: - if pair not in accepted: - nremoved += 1 - continue - av = accepted[pair] - if score != av and score != av + "L": - score = av - ncorrected += 1 - print("\t".join((a, b, score)), file=fw) - fw.close() + if pair not in accepted: + nremoved += 1 + continue + av = accepted[pair] + if score != av and score != av + "L": + score = av + ncorrected += 1 + new_block.append((a, b, score)) + if new_block: + new_blocks.append(new_block) + else: + nblocks_removed += 1 logger.debug("Removed %d existing anchors", nremoved) + if nblocks_removed: + logger.debug("Removed %d empty blocks", nblocks_removed) logger.debug("Corrected scores for %d anchors", ncorrected) + self.blocks = new_blocks + + def print_to_file(self, filename="stdout"): + """ + Print the anchors to a file, optionally filtering them based on the + accepted pairs. + """ + fw = must_open(filename, "w") + for block in self.blocks: + print("###", file=fw) + for line in block: + a, b, score = line + print("\t".join((a, b, score)), file=fw) + fw.close() + logger.debug("Anchors written to `%s`", filename) def blast(self, blastfile=None, outfile=None): diff --git a/jcvi/compara/synteny.py b/jcvi/compara/synteny.py index b039ba87..7059d93f 100755 --- a/jcvi/compara/synteny.py +++ b/jcvi/compara/synteny.py @@ -1869,9 +1869,11 @@ def liftover(args): ac.blocks[block_id].append((query, subject, str(score) + "L")) lifted += 1 - logger.debug("{} new pairs found (dist={}).".format(lifted, dist)) + logger.debug("%d new pairs found (dist=%d).", lifted, dist) newanchorfile = anchor_file.rsplit(".", 1)[0] + ".lifted.anchors" - ac.print_to_file(filename=newanchorfile, accepted=accepted) + if accepted: + ac.filter_blocks(accepted) + ac.print_to_file(filename=newanchorfile) summary([newanchorfile]) return newanchorfile diff --git a/jcvi/formats/maf.py b/jcvi/formats/maf.py index 01ed1ec5..dd63b1d8 100644 --- a/jcvi/formats/maf.py +++ b/jcvi/formats/maf.py @@ -21,6 +21,9 @@ from .base import BaseFile, logger +FLANK = 60 + + class Maf(BaseFile, dict): def __init__(self, filename, index=False): super().__init__(filename) @@ -119,10 +122,12 @@ def breakpoints(args): logger.info("Total alignments: %d", len(filtered_msa)) final = [] + # Load the sequences + ar = next(SeqIO.parse(a_fasta, "fasta")) + br = next(SeqIO.parse(b_fasta, "fasta")) for bp in bps: i = bisect(filtered_msa, (bp,)) _, arec, brec = filtered_msa[i] - logger.info("Breakpoint at %d") logger.info("%s", arec) logger.info("%s", brec) assert len(arec) == len(brec) @@ -130,15 +135,16 @@ def breakpoints(args): midpoint = len(arec) // 2 aseq = arec.seq[:midpoint] astart = arec.annotations["start"] + len(aseq) - aseq.count("-") + logger.info("%s|%s", aseq[-FLANK:], arec.seq[midpoint:][:FLANK]) bseq = brec.seq[:midpoint] bstart = brec.annotations["start"] + len(bseq) - bseq.count("-") + logger.info("%s|%s", bseq[-FLANK:], brec.seq[midpoint:][:FLANK]) bpt = Breakpoint(arec.id, astart, brec.id, bstart) + logger.info("-" * FLANK * 2 + ">") + logger.info("%s|%s", ar.seq[:astart][-FLANK:], br.seq[bstart:][:FLANK]) final.append(bpt) logger.info("Breakpoints found: %s", final) - # Load the sequences - ar = next(SeqIO.parse(a_fasta, "fasta")) - br = next(SeqIO.parse(b_fasta, "fasta")) if len(final) == 2: bp1, bp2 = final[:2] # ====-------======= diff --git a/tests/compara/synteny.py/inputs/test_empty_blocks.a.bed b/tests/compara/synteny.py/inputs/test_empty_blocks.a.bed new file mode 100644 index 00000000..f0a4f5a9 --- /dev/null +++ b/tests/compara/synteny.py/inputs/test_empty_blocks.a.bed @@ -0,0 +1,12 @@ +Chr4 54561438 54564013 evm.model.Chr4.1717 0 + +Chr4 54565362 54567326 evm.model.Chr4.1718.1 0 - +Chr4 121756560 121761288 evm.model.Chr4.3572 0 + +Chr4 121933314 121948423 evm.model.Chr4.3580 0 - +Chr4 180331940 180335210 evm.model.Chr4.5631 0 + +Chr4 180428386 180432960 evm.model.Chr4.5633 0 + +Chr4 180435251 180437141 evm.model.Chr4.5634 0 - +Chr4 217516296 217519765 evm.model.Chr4.7127 0 + +Chr4 217519781 217522525 evm.model.Chr4.7128 0 - +Chr4 227171285 227174253 evm.model.Chr4.7543 0 - +Chr4 227302006 227306154 evm.model.Chr4.7546 0 + +Chr4 231178304 231189633 evm.model.Chr4.7694 0 + diff --git a/tests/compara/synteny.py/inputs/test_empty_blocks.anchors b/tests/compara/synteny.py/inputs/test_empty_blocks.anchors new file mode 100644 index 00000000..adcf580a --- /dev/null +++ b/tests/compara/synteny.py/inputs/test_empty_blocks.anchors @@ -0,0 +1,19 @@ +### +evm.model.Chr4.5631 mrna.AA559650.t1 919 +evm.model.Chr4.5633 mrna.AA559640.t1 1600 +evm.model.Chr4.5634 mrna.AA559630.t1 571 +### +evm.model.Chr4.7694 mrna.AA560110.t1 2300 +evm.model.Chr4.7694 mrna.AA560120.t1 1410 +### +evm.model.Chr4.1717 mrna.AA564650.t1 1210 +evm.model.Chr4.1718.1 mrna.AA564640.t1 389 +### +evm.model.Chr4.7543 mrna.AA563300.t1 356 +evm.model.Chr4.7546 mrna.AA563320.t1 639 +### +evm.model.Chr4.3572 mrna.AA563680.t1 2030 +evm.model.Chr4.3580 mrna.AA563690.t1 411 +### +evm.model.Chr4.7127 mrna.AA565190.t1 1210 +evm.model.Chr4.7128 mrna.AA565170.t1 1580 diff --git a/tests/compara/synteny.py/inputs/test_empty_blocks.b.bed b/tests/compara/synteny.py/inputs/test_empty_blocks.b.bed new file mode 100644 index 00000000..a65e495e --- /dev/null +++ b/tests/compara/synteny.py/inputs/test_empty_blocks.b.bed @@ -0,0 +1,13 @@ +PKPP01013534 12975 15522 mrna.AA559630.t1 GCTI12_AA559630 + +PKPP01013534 18440 23163 mrna.AA559640.t1 GCTI12_AA559640 - +PKPP01013534 25546 29984 mrna.AA559650.t1 GCTI12_AA559650 - +PKPP01013569 17807 21064 mrna.AA560110.t1 GCTI12_AA560110 - +PKPP01013569 23741 29216 mrna.AA560120.t1 GCTI12_AA560120 - +PKPP01013816 18770 21277 mrna.AA564640.t1 GCTI12_AA564640 + +PKPP01013816 23831 25817 mrna.AA564650.t1 GCTI12_AA564650 - +PKPP01013847 17713 19380 mrna.AA563300.t1 GCTI12_AA563300 - +PKPP01013847 27303 28529 mrna.AA563320.t1 GCTI12_AA563320 + +PKPP01013878 9875 15811 mrna.AA563680.t1 GCTI12_AA563680 + +PKPP01013878 15786 19578 mrna.AA563690.t1 GCTI12_AA563690 - +PKPP01013995 6766 9385 mrna.AA565170.t1 GCTI12_AA565170 + +PKPP01013995 13891 18772 mrna.AA565190.t1 GCTI12_AA565190 - diff --git a/tests/compara/synteny.py/inputs/test_empty_blocks.last b/tests/compara/synteny.py/inputs/test_empty_blocks.last new file mode 100644 index 00000000..56678e7b --- /dev/null +++ b/tests/compara/synteny.py/inputs/test_empty_blocks.last @@ -0,0 +1,545 @@ +evm.model.000021F_np12.565 mrna.AA565170.t1 64.64 362 128 0 170 531 158 519 2.7e-40 169 +evm.model.000021F_np12.565 mrna.AA565170.t1 60.48 334 132 0 1145 1478 1145 1478 3.9e-23 112 +evm.model.000021F_np12.565 mrna.AA565170.t1 62.65 166 62 0 805 970 793 958 8.5e-10 68 +evm.model.Chr1.1874 mrna.AA563690.t1 61.52 382 141 2 527 908 482 857 3.6e-25 119 +evm.model.Chr1.1874 mrna.AA563690.t1 62.09 182 69 0 205 386 202 383 7.2e-11 71.1 +evm.model.Chr1.1874 mrna.AA563690.t1 62.43 173 65 0 915 1087 888 1060 2.2e-10 69.6 +evm.model.Chr1.2358 mrna.AA563690.t1 60.98 387 145 2 523 909 484 864 1e-23 114 +evm.model.Chr1.2358 mrna.AA563690.t1 63.24 185 68 0 208 392 211 395 3.1e-13 79.1 +evm.model.Chr1.9151 mrna.AA559640.t1 63.16 285 105 0 1158 1442 1086 1370 1.7e-25 120 +evm.model.Chr1.1966 mrna.AA564650.t1 56.03 307 132 1 1397 1703 1121 1424 0.00059 49 +evm.model.Chr1.5601 mrna.AA559650.t1 68.25 126 40 0 646 771 739 864 5.5e-12 74.3 +evm.model.Chr1.6094 mrna.AA559640.t1 59.12 296 121 0 1126 1421 1090 1385 1.7e-15 87 +evm.model.Chr1.12678 mrna.AA563690.t1 62.77 137 51 0 632 768 524 660 1.4e-06 56.9 +evm.model.Chr1.7572 mrna.AA559650.t1 61.14 175 68 0 488 662 512 686 1.1e-08 63.2 +evm.model.Chr1.5997 mrna.AA563690.t1 73.61 72 19 0 2995 3066 760 831 1.1e-05 55.3 +evm.model.Chr1.9624 mrna.AA560110.t1 60.49 243 96 0 1561 1803 1498 1740 5.1e-14 82.2 +evm.model.Chr1.9146 mrna.AA559640.t1 62.81 285 106 0 1158 1442 1086 1370 1.5e-24 117 +evm.model.Chr1.1932 mrna.AA559640.t1 56.25 272 119 0 799 1070 1102 1373 4.5e-06 55.3 +evm.model.Chr1.6455 mrna.AA559640.t1 74.33 1040 255 2 76 1112 1 1031 2.3e-224 780 +evm.model.Chr1.6455 mrna.AA559640.t1 74.10 332 86 0 1132 1463 1084 1415 4.9e-66 255 +evm.model.Chr1.6455 mrna.AA559640.t1 78.76 113 24 0 1477 1589 1456 1568 9.4e-21 104 +evm.model.Chr1.6455 mrna.AA559640.t1 68.15 157 47 1 1581 1737 1605 1758 1.3e-13 80.6 +evm.model.Chr1.2172 mrna.AA559640.t1 62.33 300 113 0 1177 1476 1087 1386 4.9e-25 119 +evm.model.Chr2.6242 mrna.AA563690.t1 75.00 68 17 0 2515 2582 751 818 9.7e-06 55.3 +evm.model.Chr2.4989 mrna.AA559640.t1 57.64 203 86 0 145 347 109 311 0.00015 50.6 +evm.model.Chr2.1750.5 mrna.AA559640.t1 63.22 348 128 0 1417 1764 1051 1398 1.6e-33 147 +evm.model.Chr2.1750.5 mrna.AA559640.t1 56.76 444 192 0 375 818 30 473 2.8e-18 96.4 +evm.model.Chr2.1750.5 mrna.AA559640.t1 60.92 238 93 0 1120 1357 781 1018 1.8e-14 83.8 +evm.model.Chr2.6418 mrna.AA559640.t1 62.86 315 117 0 1171 1485 1087 1401 2.4e-28 130 +evm.model.Chr2.6418 mrna.AA559640.t1 56.81 433 187 0 103 535 46 478 7.3e-18 94.9 +evm.model.Chr2.6418 mrna.AA559640.t1 59.92 247 99 0 826 1072 772 1018 4.3e-13 79.1 +evm.model.Chr2.8495 mrna.AA559640.t1 64.29 280 100 0 1201 1480 1096 1375 5.6e-28 128 +evm.model.Chr2.471 mrna.AA563690.t1 67.65 136 44 0 794 929 722 857 8.2e-13 77.5 +evm.model.Chr2.1765 mrna.AA563690.t1 62.95 305 107 2 1 305 520 818 1.8e-21 104 +evm.model.Chr2.1476 mrna.AA563690.t1 64.65 99 35 0 1468 1566 721 819 0.0014 47.4 +evm.model.Chr2.9100 mrna.AA563690.t1 59.51 368 143 2 386 753 503 864 9.7e-17 90.1 +evm.model.Chr2.9100 mrna.AA563690.t1 61.90 126 48 0 753 878 888 1013 0.00024 49 +evm.model.Chr2.8498 mrna.AA559640.t1 64.14 290 104 0 1201 1490 1096 1385 8.4e-29 131 +evm.model.Chr2.5229 mrna.AA563300.t1 60.16 384 153 0 46 429 16 399 5.6e-27 125 +evm.model.Chr2.5981 mrna.AA563690.t1 65.93 91 31 0 787 877 724 814 0.001 47.4 +evm.model.Chr2.1479 mrna.AA559640.t1 63.86 202 73 0 1200 1401 1197 1398 1.8e-16 90.1 +evm.model.Chr2.1761 mrna.AA563690.t1 62.95 305 107 2 1 305 520 818 1.8e-21 104 +evm.model.Chr2.4153 mrna.AA559640.t1 63.67 311 113 0 1122 1432 1086 1396 2.9e-30 136 +evm.model.Chr2.4153 mrna.AA559640.t1 60.30 335 133 0 67 401 46 380 1.2e-22 111 +evm.model.Chr2.8097 mrna.AA564640.t1 62.04 274 95 2 29 302 35 299 3.9e-15 83.8 +evm.model.Chr2.8097 mrna.AA564640.t1 69.89 93 19 1 245 337 218 301 0.00013 49 +evm.model.Chr3.2087.1 mrna.AA563690.t1 60.51 157 62 0 604 760 514 670 1.3e-05 53.8 +evm.model.Chr3.655 mrna.AA565190.t1 68.03 613 196 0 467 1079 422 1034 2.1e-95 351 +evm.model.Chr3.655 mrna.AA565190.t1 68.70 230 69 1 124 353 103 329 1.2e-27 126 +evm.model.Chr3.2949 mrna.AA564640.t1 71.29 317 82 2 1 317 1 308 9.8e-49 193 +evm.model.Chr3.5698 mrna.AA559640.t1 65.61 221 76 0 1399 1619 1165 1385 1.4e-22 111 +evm.model.Chr3.5698 mrna.AA559640.t1 59.51 284 115 0 127 410 46 329 1.9e-15 87 +evm.model.Chr3.5698 mrna.AA559640.t1 73.97 73 19 0 1098 1170 891 963 2.2e-06 56.9 +evm.model.Chr3.4229 mrna.AA559630.t1 79.45 146 13 1 1 129 277 422 4.1e-29 126 +evm.model.Chr3.4229 mrna.AA559630.t1 82.00 50 9 0 143 192 636 685 3.8e-06 52.2 +evm.model.Chr3.5695 mrna.AA559640.t1 64.71 221 78 0 160 380 1165 1385 3.8e-21 104 +evm.model.Chr3.2012 mrna.AA563680.t1 74.44 896 226 1 1276 2171 1357 2249 4.4e-195 683 +evm.model.Chr3.2012 mrna.AA563680.t1 69.25 1200 309 5 113 1252 86 1285 3.6e-193 677 +evm.model.Chr3.1490 mrna.AA563690.t1 75.32 77 19 0 1771 1847 766 842 2.9e-08 63.2 +evm.model.Chr3.1780 mrna.AA563690.t1 62.32 345 124 2 492 836 486 824 8.3e-24 114 +evm.model.Chr3.1780 mrna.AA563690.t1 59.01 161 66 0 883 1043 895 1055 0.00088 47.4 +evm.model.Chr3.5406 mrna.AA560110.t1 68.18 110 35 0 668 777 806 915 8e-09 64.8 +evm.model.Chr3.5406 mrna.AA560110.t1 65.26 95 33 0 823 917 946 1040 0.0014 47.4 +evm.model.Chr4.4391 mrna.AA560110.t1 58.73 332 137 0 674 1005 809 1140 2.1e-17 93.3 +evm.model.Chr4.7695 mrna.AA563690.t1 66.67 99 33 0 1816 1914 766 864 2.4e-05 53.8 +evm.model.Chr4.7695 mrna.AA563690.t1 60.00 155 62 0 1545 1699 498 652 0.00021 50.6 +evm.model.Chr4.1717 mrna.AA564650.t1 80.78 1238 238 0 249 1486 234 1471 0 1.21e+03 +evm.model.Chr4.1717 mrna.AA606470.t1 79.20 721 150 0 301 1021 4 724 1.2e-190 667 +evm.model.Chr4.1717 mrna.AA465890.t1 62.42 149 56 0 990 1138 972 1120 1.8e-07 60.1 +evm.model.Chr4.1717 mrna.AA152460.t1 64.34 129 46 0 1137 1265 1521 1649 1.8e-07 60.1 +evm.model.Chr4.1717 mrna.AA025990.t1 63.57 129 47 0 1137 1265 1518 1646 1.6e-06 56.9 +evm.model.Chr4.1717 mrna.AA564650.t1 65.89 129 35 1 1 129 1 120 4.8e-06 55.3 +evm.model.Chr4.1717 mrna.AA497050.t1 60.00 165 66 0 1201 1365 1552 1716 1.4e-05 53.8 +evm.model.Chr4.1717 mrna.AA261220.t1 57.58 198 84 0 1130 1327 839 1036 0.00038 49 +evm.model.Chr4.1718.1 mrna.AA564640.t1 89.87 316 29 1 10 325 7 319 6.9e-115 389 +evm.model.Chr4.1718.1 mrna.AA147060.t1 79.56 225 43 1 10 231 7 231 3.8e-51 201 +evm.model.Chr4.1718.1 mrna.AA586520.t1 63.21 280 103 0 38 317 29 308 5.4e-26 119 +evm.model.Chr4.1718.1 mrna.AA140030.t1 63.81 268 97 0 38 305 29 296 5.4e-26 119 +evm.model.Chr4.1718.1 mrna.AA036480.t1 61.84 283 108 0 43 325 430 712 1.3e-22 108 +evm.model.Chr4.1718.1 mrna.AA586520.t2 62.70 244 91 0 74 317 8 251 3.2e-20 99.6 +evm.model.Chr4.1718.1 mrna.AA570020.t1 62.90 283 102 2 42 324 33 312 8.7e-19 94.9 +evm.model.Chr4.1718.1 mrna.AA231480.t1 62.74 212 79 0 38 249 194 405 2.2e-16 87 +evm.model.Chr4.1718.1 mrna.AA116250.t1 74.76 103 26 0 221 323 2156 2258 6.1e-15 82.2 +evm.model.Chr4.1718.1 mrna.AA348660.t1 79.52 83 17 0 234 316 216 298 5.5e-14 79.1 +evm.model.Chr4.1718.1 mrna.AA348660.t1 64.42 208 68 2 97 304 97 298 1.5e-12 74.3 +evm.model.Chr4.1718.1 mrna.AA036480.t1 68.25 126 40 0 43 168 34 159 1.5e-12 74.3 +evm.model.Chr4.1718.1 mrna.AA116250.t1 79.12 91 16 1 236 323 2195 2285 1.5e-12 74.3 +evm.model.Chr4.1718.1 mrna.AA564640.t1 83.82 68 11 0 229 296 250 317 1.5e-12 74.3 +evm.model.Chr4.1718.1 mrna.AA116250.t1 74.29 105 24 1 221 322 2165 2269 1.4e-11 71.1 +evm.model.Chr4.1718.1 mrna.AA116250.t1 80.00 85 14 1 236 317 2141 2225 1.4e-11 71.1 +evm.model.Chr4.1718.1 mrna.AA564640.t1 78.67 75 16 0 253 327 226 300 4.2e-11 69.6 +evm.model.Chr4.1718.1 mrna.AA372450.t1 86.21 58 8 0 260 317 566 623 1.3e-10 68 +evm.model.Chr4.1718.1 mrna.AA348660.t2 78.87 71 15 0 246 316 108 178 3.8e-10 66.4 +evm.model.Chr4.1718.1 mrna.AA116250.t1 73.96 96 22 1 229 321 2200 2295 3.5e-09 63.2 +evm.model.Chr4.1718.1 mrna.AA348660.t2 77.46 71 16 0 234 304 108 178 3.5e-09 63.2 +evm.model.Chr4.1718.1 mrna.AA564640.t1 85.71 63 6 1 265 327 226 285 1e-08 61.7 +evm.model.Chr4.1718.1 mrna.AA528880.t1 67.96 103 33 0 220 322 1460 1562 3.2e-08 60.1 +evm.model.Chr4.1718.1 mrna.AA564640.t1 82.46 57 10 0 229 285 262 318 3.2e-08 60.1 +evm.model.Chr4.1718.1 mrna.AA372450.t1 84.91 53 8 0 272 324 563 615 3.2e-08 60.1 +evm.model.Chr4.1718.1 mrna.AA348660.t1 73.08 78 21 0 246 323 216 293 9.5e-08 58.5 +evm.model.Chr4.1718.1 mrna.AA586520.t1 80.36 56 11 0 262 317 226 281 8.7e-07 55.3 +evm.model.Chr4.1718.1 mrna.AA586520.t2 80.36 56 11 0 262 317 169 224 8.7e-07 55.3 +evm.model.Chr4.1718.1 mrna.AA116250.t1 72.22 90 22 1 220 306 2206 2295 2.6e-06 53.8 +evm.model.Chr4.1718.1 mrna.AA570020.t1 70.53 95 25 1 220 311 301 395 7.9e-06 52.2 +evm.model.Chr4.1718.1 mrna.AA062190.t1 69.14 81 25 0 230 310 137 217 2.4e-05 50.6 +evm.model.Chr4.1718.1 mrna.AA139140.t1 69.62 79 24 0 233 311 431 509 2.4e-05 50.6 +evm.model.Chr4.1718.1 mrna.AA528880.t1 69.89 93 26 1 215 307 1472 1562 7.2e-05 49 +evm.model.Chr4.1718.1 mrna.AA348660.t2 72.73 66 18 0 258 323 108 173 7.2e-05 49 +evm.model.Chr4.1718.1 mrna.AA348660.t1 80.00 50 10 0 275 324 218 267 7.2e-05 49 +evm.model.Chr4.1718.1 mrna.AA116250.t1 84.09 44 7 0 280 323 2134 2177 7.2e-05 49 +evm.model.Chr4.1718.1 mrna.AA438190.t1 69.57 92 27 1 233 323 2431 2522 0.00022 47.4 +evm.model.Chr4.1718.1 mrna.AA512970.t1 69.57 92 27 1 233 323 2434 2525 0.00022 47.4 +evm.model.Chr4.3580 mrna.AA446740.t1 75.35 852 207 1 394 1245 139 987 3.3e-192 674 +evm.model.Chr4.3580 mrna.AA563690.t1 83.46 387 64 0 670 1056 478 864 4.4e-113 411 +evm.model.Chr4.3580 mrna.AA238660.t1 64.30 860 301 2 361 1214 217 1076 3.2e-100 368 +evm.model.Chr4.3580 mrna.AA054990.t1 63.95 871 308 2 359 1223 173 1043 8.7e-99 364 +evm.model.Chr4.3580 mrna.AA230140.t1 64.06 832 293 2 353 1178 233 1064 1.7e-94 349 +evm.model.Chr4.3580 mrna.AA563690.t1 76.13 398 92 1 1506 1900 1245 1642 1.9e-85 319 +evm.model.Chr4.3580 mrna.AA054990.t2 64.85 680 233 2 550 1223 1 680 3e-79 299 +evm.model.Chr4.3580 mrna.AA563690.t1 74.94 391 68 2 181 556 31 406 6.5e-76 288 +evm.model.Chr4.3580 mrna.AA563690.t1 78.87 336 50 2 1056 1373 888 1220 2e-75 286 +evm.model.Chr4.3580 mrna.AA460080.t1 65.49 510 176 0 353 862 221 730 6e-65 251 +evm.model.Chr4.3580 mrna.AA477900.t1 65.63 483 166 0 367 849 205 687 1.3e-61 240 +evm.model.Chr4.3580 mrna.AA049090.t1 66.59 449 150 0 370 818 199 647 1.2e-60 237 +evm.model.Chr4.3580 mrna.AA497850.t1 66.74 430 143 0 353 782 533 962 2.8e-58 229 +evm.model.Chr4.3580 mrna.AA612290.t1 76.72 262 61 0 669 930 207 468 2.2e-56 223 +evm.model.Chr4.3580 mrna.AA152590.t1 64.84 455 160 0 394 848 268 722 5.4e-54 215 +evm.model.Chr4.3580 mrna.AA460080.t1 68.22 321 102 0 912 1232 786 1106 2e-45 187 +evm.model.Chr4.3580 mrna.AA304340.t1 64.89 376 132 0 487 862 382 757 4.9e-43 179 +evm.model.Chr4.3580 mrna.AA324320.t1 69.49 272 83 0 541 812 118 389 3.6e-40 169 +evm.model.Chr4.3580 mrna.AA109910.t1 68.59 277 87 0 394 670 238 514 9.6e-39 164 +evm.model.Chr4.3580 mrna.AA612290.t1 73.71 213 56 0 1033 1245 475 687 8.6e-38 161 +evm.model.Chr4.3580 mrna.AA052160.t2 66.03 312 106 0 912 1223 762 1073 2.6e-37 160 +evm.model.Chr4.3580 mrna.AA249880.t1 65.20 319 111 0 353 671 155 473 6.9e-36 155 +evm.model.Chr4.3580 mrna.AA152590.t1 64.24 316 113 0 913 1228 793 1108 1.5e-32 144 +evm.model.Chr4.3580 mrna.AA049090.t1 63.44 320 117 0 913 1232 748 1067 1.2e-30 138 +evm.model.Chr4.3580 mrna.AA414840.t1 61.81 364 133 2 700 1057 349 712 5.7e-24 115 +evm.model.Chr4.3580 mrna.AA324320.t1 63.53 266 97 0 913 1178 496 761 5.7e-24 115 +evm.model.Chr4.3580 mrna.AA036560.t1 60.86 327 128 0 919 1245 397 723 1.7e-23 114 +evm.model.Chr4.3580 mrna.AA395800.t1 60.86 327 128 0 919 1245 346 672 1.7e-23 114 +evm.model.Chr4.3580 mrna.AA563690.t1 70.52 173 51 0 1653 1825 1575 1747 1.7e-23 114 +evm.model.Chr4.3580 mrna.AA414840.t1 61.88 341 124 2 712 1046 1 341 1.4e-21 108 +evm.model.Chr4.3580 mrna.AA052160.t1 63.95 233 84 0 991 1223 778 1010 1.2e-20 104 +evm.model.Chr4.3580 mrna.AA295810.t1 64.62 212 75 0 474 685 339 550 3.3e-19 99.6 +evm.model.Chr4.3580 mrna.AA147280.t1 57.32 553 223 3 471 1018 618 1162 3e-18 96.4 +evm.model.Chr4.3580 mrna.AA019210.t1 56.43 521 221 1 700 1214 685 1205 3e-18 96.4 +evm.model.Chr4.3580 mrna.AA263320.t1 65.35 202 67 1 916 1117 1648 1846 7.1e-16 88.5 +evm.model.Chr4.3580 mrna.AA198030.t1 60.18 334 124 2 525 858 399 723 2.1e-15 87 +evm.model.Chr4.3580 mrna.AA046330.t1 61.45 262 98 1 375 636 426 684 6.4e-15 85.4 +evm.model.Chr4.3580 mrna.AA046330.t2 61.45 262 98 1 375 636 426 684 6.4e-15 85.4 +evm.model.Chr4.3580 mrna.AA241250.t1 61.45 262 98 1 375 636 321 579 6.4e-15 85.4 +evm.model.Chr4.3580 mrna.AA504540.t1 59.88 334 125 2 525 858 399 723 1.9e-14 83.8 +evm.model.Chr4.3580 mrna.AA046490.t1 58.95 324 127 1 528 851 204 521 5.7e-14 82.2 +evm.model.Chr4.3580 mrna.AA056240.t1 66.03 156 53 0 958 1113 799 954 1.7e-13 80.6 +evm.model.Chr4.3580 mrna.AA506580.t1 63.86 202 70 1 916 1117 1651 1849 5.1e-13 79.1 +evm.model.Chr4.3580 mrna.AA255240.t1 56.67 487 198 3 529 1010 352 830 1.2e-10 71.1 +evm.model.Chr4.3580 mrna.AA301730.t1 57.47 388 159 2 626 1010 2195 2579 1.2e-10 71.1 +evm.model.Chr4.3580 mrna.AA052570.t1 57.33 300 128 0 915 1214 795 1094 1.2e-10 71.1 +evm.model.Chr4.3580 mrna.AA154240.t1 61.38 246 91 2 412 656 526 768 1.1e-09 68 +evm.model.Chr4.3580 mrna.AA293790.t1 66.67 147 48 1 951 1097 1113 1258 1.1e-09 68 +evm.model.Chr4.3580 mrna.AA327180.t1 66.40 125 42 0 1057 1181 394 518 3.3e-09 66.4 +evm.model.Chr4.3580 mrna.AA058480.t1 56.94 288 124 0 574 861 649 936 1e-08 64.8 +evm.model.Chr4.3580 mrna.AA183750.t1 61.90 168 64 0 1056 1223 735 902 1e-08 64.8 +evm.model.Chr4.3580 mrna.AA385950.t1 63.16 152 56 0 484 635 412 563 1e-08 64.8 +evm.model.Chr4.3580 mrna.AA416400.t1 63.89 144 52 0 915 1058 744 887 1e-08 64.8 +evm.model.Chr4.3580 mrna.AA416400.t2 63.89 144 52 0 915 1058 744 887 1e-08 64.8 +evm.model.Chr4.3580 mrna.AA416400.t3 63.89 144 52 0 915 1058 744 887 1e-08 64.8 +evm.model.Chr4.3580 mrna.AA410060.t1 67.24 116 38 0 955 1070 1252 1367 1e-08 64.8 +evm.model.Chr4.3580 mrna.AA444750.t1 75.64 78 19 0 930 1007 2244 2321 1e-08 64.8 +evm.model.Chr4.3580 mrna.AA163920.t1 56.70 291 126 0 568 858 145 435 3e-08 63.2 +evm.model.Chr4.3580 mrna.AA186280.t1 59.13 252 100 1 381 632 786 1034 3e-08 63.2 +evm.model.Chr4.3580 mrna.AA186280.t2 59.13 252 100 1 381 632 204 452 3e-08 63.2 +evm.model.Chr4.3580 mrna.AA344780.t1 62.58 155 58 0 916 1070 715 869 3e-08 63.2 +evm.model.Chr4.3580 mrna.AA431630.t1 66.96 115 38 0 524 638 452 566 3e-08 63.2 +evm.model.Chr4.3580 mrna.AA461400.t1 66.96 115 38 0 524 638 452 566 3e-08 63.2 +evm.model.Chr4.3580 mrna.AA154700.t1 79.10 67 14 0 952 1018 2563 2629 3e-08 63.2 +evm.model.Chr4.3580 mrna.AA116920.t1 63.38 142 52 0 915 1056 822 963 9e-08 61.7 +evm.model.Chr4.3580 mrna.AA014740.t1 64.84 128 45 0 511 638 1963 2090 9e-08 61.7 +evm.model.Chr4.3580 mrna.AA133400.t1 62.94 143 53 0 528 670 1614 1756 2.7e-07 60.1 +evm.model.Chr4.3580 mrna.AA133400.t2 62.94 143 53 0 528 670 972 1114 2.7e-07 60.1 +evm.model.Chr4.3580 mrna.AA380670.t1 67.29 107 35 0 915 1021 1629 1735 2.7e-07 60.1 +evm.model.Chr4.3580 mrna.AA261900.t1 89.36 47 5 0 1453 1407 29 75 2.7e-07 60.1 +evm.model.Chr4.3580 mrna.AA227640.t1 57.09 254 109 0 568 821 592 845 8e-07 58.5 +evm.model.Chr4.3580 mrna.AA465610.t1 61.11 162 63 0 915 1076 726 887 8e-07 58.5 +evm.model.Chr4.3580 mrna.AA465610.t1 67.31 104 34 0 715 818 520 623 8e-07 58.5 +evm.model.Chr4.3580 mrna.AA465610.t2 67.31 104 34 0 715 818 520 623 8e-07 58.5 +evm.model.Chr4.3580 mrna.AA587840.t1 67.31 104 34 0 715 818 520 623 8e-07 58.5 +evm.model.Chr4.3580 mrna.AA335590.t1 68.37 98 31 0 916 1013 1300 1397 8e-07 58.5 +evm.model.Chr4.3580 mrna.AA335590.t1 68.37 98 31 0 916 1013 1621 1718 8e-07 58.5 +evm.model.Chr4.3580 mrna.AA446530.t1 69.57 92 28 0 958 1049 760 851 8e-07 58.5 +evm.model.Chr4.3580 mrna.AA586870.t1 73.68 76 20 0 568 643 295 370 8e-07 58.5 +evm.model.Chr4.3580 mrna.AA028490.t1 57.29 384 146 3 482 853 302 679 2.4e-06 56.9 +evm.model.Chr4.3580 mrna.AA304340.t1 68.82 93 29 0 367 459 286 378 2.4e-06 56.9 +evm.model.Chr4.3580 mrna.AA268110.t1 61.33 150 58 0 709 858 2059 2208 7.2e-06 55.3 +evm.model.Chr4.3580 mrna.AA317530.t1 61.33 150 58 0 709 858 2089 2238 7.2e-06 55.3 +evm.model.Chr4.3580 mrna.AA431630.t1 61.81 144 55 0 915 1058 837 980 7.2e-06 55.3 +evm.model.Chr4.3580 mrna.AA563690.t1 71.79 78 22 0 1996 2073 1753 1830 7.2e-06 55.3 +evm.model.Chr4.3580 mrna.AA193980.t1 88.64 44 5 0 1408 1451 1702 1745 7.2e-06 55.3 +evm.model.Chr4.3580 mrna.AA506310.t1 62.66 158 56 1 484 638 1582 1739 2.2e-05 53.8 +evm.model.Chr4.3580 mrna.AA011880.t1 61.54 143 55 0 694 836 1735 1877 2.2e-05 53.8 +evm.model.Chr4.3580 mrna.AA320860.t1 62.22 135 51 0 484 618 307 441 2.2e-05 53.8 +evm.model.Chr4.3580 mrna.AA381370.t1 68.54 89 28 0 916 1004 1444 1532 2.2e-05 53.8 +evm.model.Chr4.3580 mrna.AA392240.t1 73.24 71 19 0 568 638 340 410 2.2e-05 53.8 +evm.model.Chr4.3580 mrna.AA036560.t1 75.38 65 16 0 481 545 217 281 2.2e-05 53.8 +evm.model.Chr4.3580 mrna.AA395800.t1 75.38 65 16 0 481 545 166 230 2.2e-05 53.8 +evm.model.Chr4.3580 mrna.AA427600.t1 90.24 41 4 0 1453 1413 32 72 2.2e-05 53.8 +evm.model.Chr4.3580 mrna.AA376280.t1 58.99 217 86 1 422 638 2981 3194 6.5e-05 52.2 +evm.model.Chr4.3580 mrna.AA327710.t1 60.39 154 61 0 700 853 547 700 6.5e-05 52.2 +evm.model.Chr4.3580 mrna.AA461400.t1 61.11 144 56 0 915 1058 837 980 6.5e-05 52.2 +evm.model.Chr4.3580 mrna.AA502780.t1 61.27 142 55 0 529 670 1567 1708 6.5e-05 52.2 +evm.model.Chr4.3580 mrna.AA411430.t1 68.60 86 27 0 916 1001 1657 1742 6.5e-05 52.2 +evm.model.Chr4.3580 mrna.AA015600.t1 80.77 52 10 0 957 1008 807 858 6.5e-05 52.2 +evm.model.Chr4.3580 mrna.AA455280.t1 84.78 46 7 0 958 1003 2599 2644 6.5e-05 52.2 +evm.model.Chr4.3580 mrna.AA097090.t1 59.41 202 79 1 440 638 1544 1745 0.00019 50.6 +evm.model.Chr4.3580 mrna.AA479490.t1 62.03 158 57 1 484 638 1582 1739 0.00019 50.6 +evm.model.Chr4.3580 mrna.AA543240.t1 71.23 73 21 0 944 1016 2258 2330 0.00019 50.6 +evm.model.Chr4.3580 mrna.AA025400.t1 73.13 67 18 0 568 634 292 358 0.00019 50.6 +evm.model.Chr4.3580 mrna.AA083300.t1 75.41 61 15 0 943 1003 1594 1654 0.00019 50.6 +evm.model.Chr4.3580 mrna.AA582230.t1 75.41 61 15 0 943 1003 949 1009 0.00019 50.6 +evm.model.Chr4.3580 mrna.AA284380.t1 76.27 59 14 0 957 1015 2589 2647 0.00019 50.6 +evm.model.Chr4.3580 mrna.AA286490.t1 86.05 43 6 0 1409 1451 29 71 0.00019 50.6 +evm.model.Chr4.3580 mrna.AA198610.t1 87.80 41 5 0 1451 1411 22 62 0.00019 50.6 +evm.model.Chr4.3580 mrna.AA387850.t1 62.64 174 57 2 567 739 1236 1402 0.00058 49 +evm.model.Chr4.3580 mrna.AA387850.t1 62.64 174 57 2 567 739 3066 3232 0.00058 49 +evm.model.Chr4.3580 mrna.AA021280.t1 67.44 86 28 0 916 1001 1417 1502 0.00058 49 +evm.model.Chr4.3580 mrna.AA439030.t1 70.27 74 22 0 1378 1451 130 203 0.00058 49 +evm.model.Chr4.3580 mrna.AA452510.t1 82.61 46 8 0 1398 1443 24 69 0.00058 49 +evm.model.Chr4.3580 mrna.AA213330.t1 85.71 42 6 0 1408 1449 1045 1086 0.00058 49 +evm.model.Chr4.3580 mrna.AA279220.t1 57.76 232 95 1 440 671 1487 1715 0.0017 47.4 +evm.model.Chr4.3580 mrna.AA027020.t1 61.42 127 49 0 727 853 586 712 0.0017 47.4 +evm.model.Chr4.3580 mrna.AA329290.t1 69.86 73 22 0 782 854 1361 1433 0.0017 47.4 +evm.model.Chr4.3580 mrna.AA082620.t1 71.64 67 19 0 941 1007 2363 2429 0.0017 47.4 +evm.model.Chr4.3580 mrna.AA403490.t1 71.64 67 19 0 950 1016 2066 2132 0.0017 47.4 +evm.model.Chr4.3580 mrna.AA006490.t1 74.58 59 15 0 694 752 388 446 0.0017 47.4 +evm.model.Chr4.3580 mrna.AA220860.t1 75.44 57 14 0 958 1014 2407 2463 0.0017 47.4 +evm.model.Chr4.3580 mrna.AA277750.t1 77.36 53 12 0 958 1010 106 158 0.0017 47.4 +evm.model.Chr4.3580 mrna.AA202760.t1 78.43 51 11 0 689 739 1655 1705 0.0017 47.4 +evm.model.Chr4.3580 mrna.AA160640.t1 82.22 45 8 0 1407 1451 120 164 0.0017 47.4 +evm.model.Chr4.7543 mrna.AA127150.t1 73.95 933 210 6 59 979 2 913 6.3e-183 642 +evm.model.Chr4.7543 mrna.AA563300.t1 70.51 546 161 0 41 586 14 559 1.4e-96 356 +evm.model.Chr4.7543 mrna.AA562860.t1 79.05 377 79 0 175 551 169 545 3.3e-94 348 +evm.model.Chr4.7543 mrna.AA269040.t1 70.47 508 150 0 79 586 1 508 5.8e-89 330 +evm.model.Chr4.7543 mrna.AA127150.t1 73.85 436 93 3 1167 1593 1251 1674 5.9e-79 297 +evm.model.Chr4.7543 mrna.AA505580.t1 62.60 516 193 0 34 549 37 552 8.9e-52 207 +evm.model.Chr4.7543 mrna.AA550780.t1 62.21 516 195 0 34 549 37 552 7.2e-50 201 +evm.model.Chr4.7543 mrna.AA473050.t1 83.33 168 28 0 381 548 150 317 3.4e-43 179 +evm.model.Chr4.7543 mrna.AA473050.t1 80.00 130 26 0 174 303 24 153 5.4e-27 125 +evm.model.Chr4.7543 mrna.AA345400.t1 77.59 116 26 0 59 174 2 117 2.6e-20 103 +evm.model.Chr4.7543 mrna.AA127150.t1 76.47 102 24 0 925 1026 1114 1215 1.5e-15 87 +evm.model.Chr4.7543 mrna.AA269040.t1 81.33 75 14 0 1518 1592 1074 1148 3.3e-12 75.9 +evm.model.Chr4.7543 mrna.AA563300.t1 80.00 75 15 0 1518 1592 1125 1199 2.9e-11 72.7 +evm.model.Chr4.7543 mrna.AA244440.t1 55.95 370 163 0 34 403 88 457 8.8e-11 71.1 +evm.model.Chr4.7543 mrna.AA127150.t1 83.33 66 11 0 1082 1147 1139 1204 8.8e-11 71.1 +evm.model.Chr4.7543 mrna.AA244440.t2 57.14 280 120 0 124 403 10 289 7.1e-09 64.8 +evm.model.Chr4.7543 mrna.AA244440.t3 57.14 280 120 0 124 403 10 289 7.1e-09 64.8 +evm.model.Chr4.7543 mrna.AA127150.t1 77.38 84 16 1 952 1032 1033 1116 2.1e-08 63.2 +evm.model.Chr4.7543 mrna.AA442990.t1 63.49 126 46 0 278 403 17 142 5.1e-06 55.3 +evm.model.Chr4.6663 mrna.AA564640.t1 85.51 69 10 0 243 311 231 299 7.7e-14 79.1 +evm.model.Chr4.6663 mrna.AA564640.t1 79.37 63 13 0 243 305 255 317 4.3e-08 60.1 +evm.model.Chr4.6663 mrna.AA564640.t1 84.31 51 8 0 243 293 243 293 3.9e-07 56.9 +evm.model.Chr4.6663 mrna.AA564640.t1 71.58 95 24 1 221 312 194 288 1.2e-06 55.3 +evm.model.Chr4.6663 mrna.AA564640.t1 77.97 59 13 0 253 311 217 275 3.5e-06 53.8 +evm.model.Chr4.7128 mrna.AA021680.t1 79.05 1819 375 1 143 1961 134 1946 0 1.66e+03 +evm.model.Chr4.7128 mrna.AA565170.t1 79.02 1735 361 1 237 1971 24 1755 0 1.58e+03 +evm.model.Chr4.7128 mrna.AA314890.t1 72.12 373 104 0 403 775 142 514 2.4e-68 262 +evm.model.Chr4.7128 mrna.AA545280.t1 77.53 178 40 0 900 1077 120 297 2e-36 157 +evm.model.Chr4.7128 mrna.AA156950.t1 71.69 166 47 0 1675 1840 568 733 5e-24 115 +evm.model.Chr4.5634 mrna.AA559630.t1 84.25 546 80 2 1 543 277 819 1.2e-168 571 +evm.model.Chr4.5634 mrna.AA215130.t1 85.51 138 20 0 1 138 1 138 3.9e-37 157 +evm.model.Chr4.5634 mrna.AA215130.t2 70.45 132 33 1 277 402 139 270 9.7e-13 75.9 +evm.model.Chr4.5634 mrna.AA215130.t1 69.70 132 34 1 277 402 256 387 8.8e-12 72.7 +evm.model.Chr4.5634 mrna.AA161320.t1 74.36 78 20 0 49 126 40 117 1.9e-08 61.7 +evm.model.Chr4.1865 mrna.AA564640.t1 68.80 125 39 0 10 134 115 239 6.6e-13 75.9 +evm.model.Chr4.5633 mrna.AA559640.t1 85.28 1433 211 0 1 1433 1 1433 0 1.6e+03 +evm.model.Chr4.5633 mrna.AA393070.t2 75.85 1035 238 2 6 1031 81 1112 3.6e-238 825 +evm.model.Chr4.5633 mrna.AA393070.t1 75.63 1038 238 3 6 1031 81 1115 2.1e-233 810 +evm.model.Chr4.5633 mrna.AA215110.t1 75.12 1013 246 2 569 1581 560 1566 9.2e-226 784 +evm.model.Chr4.5633 mrna.AA215110.t1 76.91 498 115 0 8 505 62 559 1.7e-117 425 +evm.model.Chr4.5633 mrna.AA466250.t1 86.00 300 42 0 36 335 1701 2000 1e-92 343 +evm.model.Chr4.5633 mrna.AA559640.t1 81.27 331 53 1 1464 1794 1437 1758 4.4e-85 318 +evm.model.Chr4.5633 mrna.AA393070.t1 76.72 335 78 0 1080 1414 1131 1465 4.5e-75 285 +evm.model.Chr4.5633 mrna.AA393070.t2 76.72 335 78 0 1080 1414 1128 1462 4.5e-75 285 +evm.model.Chr4.5633 mrna.AA040620.t1 64.84 310 109 0 1077 1386 636 945 1.3e-33 147 +evm.model.Chr4.5633 mrna.AA218160.t1 63.39 336 123 0 1059 1394 1146 1481 1.2e-32 144 +evm.model.Chr4.5633 mrna.AA218160.t2 63.39 336 123 0 1059 1394 1146 1481 1.2e-32 144 +evm.model.Chr4.5633 mrna.AA074560.t1 65.17 290 101 0 1105 1394 1024 1313 1.1e-31 141 +evm.model.Chr4.5633 mrna.AA349350.t1 63.03 330 122 0 38 367 65 394 9.6e-31 138 +evm.model.Chr4.5633 mrna.AA349350.t2 63.03 330 122 0 38 367 527 856 9.6e-31 138 +evm.model.Chr4.5633 mrna.AA349350.t1 62.76 333 124 0 1062 1394 1101 1433 2.9e-30 136 +evm.model.Chr4.5633 mrna.AA349350.t2 62.76 333 124 0 1062 1394 1563 1895 2.9e-30 136 +evm.model.Chr4.5633 mrna.AA614110.t1 61.69 355 136 0 1063 1417 1072 1426 2.6e-29 133 +evm.model.Chr4.5633 mrna.AA074560.t1 59.57 423 171 0 50 472 77 499 2.3e-28 130 +evm.model.Chr4.5633 mrna.AA328120.t1 62.99 308 114 0 1090 1397 1147 1454 6.9e-28 128 +evm.model.Chr4.5633 mrna.AA277880.t1 58.74 446 184 0 13 458 34 479 6.2e-27 125 +evm.model.Chr4.5633 mrna.AA306110.t1 58.74 446 184 0 13 458 34 479 6.2e-27 125 +evm.model.Chr4.5633 mrna.AA015780.t1 62.33 300 113 0 1087 1386 1210 1509 5e-25 119 +evm.model.Chr4.5633 mrna.AA407430.t1 61.32 318 123 0 1096 1413 1198 1515 4.5e-24 115 +evm.model.Chr4.5633 mrna.AA266680.t1 62.00 300 114 0 1087 1386 1099 1398 4.5e-24 115 +evm.model.Chr4.5633 mrna.AA395080.t1 61.36 308 119 0 1090 1397 1207 1514 4e-23 112 +evm.model.Chr4.5633 mrna.AA320210.t1 62.07 290 110 0 1096 1385 1237 1526 4e-23 112 +evm.model.Chr4.5633 mrna.AA393070.t1 73.46 162 40 1 1636 1794 1579 1740 1.2e-22 111 +evm.model.Chr4.5633 mrna.AA393070.t2 73.46 162 40 1 1636 1794 1576 1737 1.2e-22 111 +evm.model.Chr4.5633 mrna.AA144960.t1 61.33 300 116 0 1086 1385 1110 1409 3.6e-22 109 +evm.model.Chr4.5633 mrna.AA215110.t1 74.83 151 35 1 1644 1794 1674 1821 3.6e-22 109 +evm.model.Chr4.5633 mrna.AA218160.t1 57.82 422 178 0 52 473 106 527 3.3e-21 106 +evm.model.Chr4.5633 mrna.AA218160.t2 57.82 422 178 0 52 473 106 527 3.3e-21 106 +evm.model.Chr4.5633 mrna.AA279480.t1 61.40 285 110 0 1102 1386 1156 1440 9.7e-21 104 +evm.model.Chr4.5633 mrna.AA242940.t1 63.33 240 88 0 1178 1417 1319 1558 2.9e-20 103 +evm.model.Chr4.5633 mrna.AA002200.t1 60.19 309 123 0 46 354 103 411 8.7e-20 101 +evm.model.Chr4.5633 mrna.AA002200.t2 60.19 309 123 0 46 354 103 411 8.7e-20 101 +evm.model.Chr4.5633 mrna.AA111460.t1 64.22 218 78 0 1180 1397 130 347 2.6e-19 99.6 +evm.model.Chr4.5633 mrna.AA393070.t1 79.81 104 21 0 1480 1583 1477 1580 2.6e-19 99.6 +evm.model.Chr4.5633 mrna.AA393070.t2 79.81 104 21 0 1480 1583 1474 1577 2.6e-19 99.6 +evm.model.Chr4.5633 mrna.AA451620.t1 57.98 426 176 1 13 435 46 471 7.9e-19 98 +evm.model.Chr4.5633 mrna.AA095590.t1 60.70 285 112 0 1113 1397 1224 1508 7.9e-19 98 +evm.model.Chr4.5633 mrna.AA167570.t1 60.00 300 120 0 1086 1385 1086 1385 2.4e-18 96.4 +evm.model.Chr4.5633 mrna.AA304940.t1 60.34 290 115 0 1096 1385 1180 1469 2.4e-18 96.4 +evm.model.Chr4.5633 mrna.AA304940.t2 60.34 290 115 0 1096 1385 904 1193 2.4e-18 96.4 +evm.model.Chr4.5633 mrna.AA463560.t1 56.97 423 182 0 13 435 262 684 7e-18 94.9 +evm.model.Chr4.5633 mrna.AA444970.t1 58.75 320 132 0 46 365 124 443 1.9e-16 90.1 +evm.model.Chr4.5633 mrna.AA144960.t1 65.56 180 62 0 186 365 57 236 1.9e-16 90.1 +evm.model.Chr4.5633 mrna.AA242940.t1 56.09 419 184 0 55 473 112 530 4.6e-14 82.2 +evm.model.Chr4.5633 mrna.AA614110.t1 56.09 419 184 0 55 473 40 458 4.6e-14 82.2 +evm.model.Chr4.5633 mrna.AA266680.t1 64.85 165 58 0 150 314 171 335 4.1e-13 79.1 +evm.model.Chr4.5633 mrna.AA015780.t1 61.99 221 81 1 97 314 124 344 1.1e-11 74.3 +evm.model.Chr4.5633 mrna.AA468530.t1 60.95 210 82 0 97 306 127 336 1.1e-11 74.3 +evm.model.Chr4.5633 mrna.AA468530.t2 60.95 210 82 0 97 306 430 639 1.1e-11 74.3 +evm.model.Chr4.5633 mrna.AA167570.t1 66.92 130 43 0 193 322 217 346 9.9e-11 71.1 +evm.model.Chr4.5633 mrna.AA468530.t3 60.19 206 82 0 101 306 5 210 8.9e-10 68 +evm.model.Chr4.5633 mrna.AA468530.t4 60.19 206 82 0 101 306 5 210 8.9e-10 68 +evm.model.Chr4.5633 mrna.AA074560.t1 58.87 231 95 0 781 1011 778 1008 2.7e-09 66.4 +evm.model.Chr4.5633 mrna.AA038930.t1 63.06 157 58 0 179 335 203 359 2.7e-09 66.4 +evm.model.Chr4.5633 mrna.AA279480.t1 62.84 148 55 0 186 333 228 375 7.2e-08 61.7 +evm.model.Chr4.5633 mrna.AA466850.t1 59.57 188 76 0 1183 1370 517 704 6.4e-07 58.5 +evm.model.Chr4.5633 mrna.AA051080.t1 62.77 137 51 0 175 311 202 338 1.9e-06 56.9 +evm.model.Chr4.5633 mrna.AA335430.t1 64.46 121 43 0 210 330 234 354 1.9e-06 56.9 +evm.model.Chr4.5633 mrna.AA144960.t1 68.75 112 32 1 891 1002 879 987 1.9e-06 56.9 +evm.model.Chr4.5633 mrna.AA395080.t1 55.63 284 126 0 182 465 260 543 5.2e-05 52.2 +evm.model.Chr4.5633 mrna.AA269720.t1 65.35 101 35 0 1286 1386 503 603 0.00016 50.6 +evm.model.Chr4.5633 mrna.AA320210.t1 62.61 115 43 0 893 1007 980 1094 0.0014 47.4 +evm.model.Chr4.7618 mrna.AA564640.t1 74.24 66 17 0 600 665 246 311 5.8e-05 52.2 +evm.model.Chr4.7618 mrna.AA564640.t1 73.13 67 18 0 614 680 245 311 0.00017 50.6 +evm.model.Chr4.5631 mrna.AA559650.t1 83.73 891 130 3 1 879 1 888 8.2e-276 919 +evm.model.Chr4.5631 mrna.AA421000.t1 69.60 125 38 0 730 854 754 878 1.9e-13 79.1 +evm.model.Chr4.5631 mrna.AA098200.t1 58.73 189 78 0 502 690 520 708 8.2e-06 53.8 +evm.model.Chr4.5631 mrna.AA467330.t1 58.73 189 78 0 502 690 217 405 8.2e-06 53.8 +evm.model.Chr4.5631 mrna.AA368130.t1 71.43 77 22 0 601 677 583 659 8.2e-06 53.8 +evm.model.Chr4.5631 mrna.AA474860.t1 71.43 77 22 0 601 677 586 662 8.2e-06 53.8 +evm.model.Chr4.5631 mrna.AA263850.t1 74.63 67 17 0 599 665 518 584 8.2e-06 53.8 +evm.model.Chr4.5631 mrna.AA421000.t1 83.72 43 7 0 623 665 560 602 0.00066 47.4 +evm.model.Chr4.5631 mrna.AA504380.t1 83.72 43 7 0 623 665 527 569 0.00066 47.4 +evm.model.Chr4.7038 mrna.AA564650.t1 71.64 67 19 0 1084 1150 1162 1228 0.0011 47.4 +evm.model.Chr4.5402 mrna.AA559640.t1 59.68 310 125 0 1088 1397 1076 1385 2.3e-18 96.4 +evm.model.Chr4.7546 mrna.AA514510.t1 85.87 899 118 2 1 893 1 896 3.2e-301 999 +evm.model.Chr4.7546 mrna.AA563320.t1 72.62 891 244 0 1 891 1 891 9.3e-183 639 +evm.model.Chr4.7546 mrna.AA269030.t1 72.30 888 246 0 1 888 1 888 2.2e-179 628 +evm.model.Chr4.7546 mrna.AA342060.t1 87.50 320 37 1 565 884 1 317 2.9e-101 370 +evm.model.Chr4.7692 mrna.AA560110.t1 88.57 1890 210 1 26 1909 17 1906 0 2.3e+03 +evm.model.Chr4.5256 mrna.AA563690.t1 64.75 122 43 0 1882 2003 535 656 9.5e-07 58.5 +evm.model.Chr4.1191 mrna.AA564650.t1 59.47 190 77 0 1313 1502 1085 1274 1.6e-06 58.5 +evm.model.Chr4.7693 mrna.AA560120.t1 88.40 1172 130 1 21 1192 27 1192 0 1.41e+03 +evm.model.Chr4.4651 mrna.AA559650.t1 70.13 77 23 0 592 668 610 686 6.8e-05 50.6 +evm.model.Chr4.1465 mrna.AA563690.t1 55.69 325 141 1 431 755 503 824 0.00029 49 +evm.model.Chr4.51 mrna.AA563690.t1 76.79 56 13 0 685 740 766 821 0.00025 49 +evm.model.Chr4.7694 mrna.AA387760.t1 82.31 2097 365 1 1 2091 1 2097 0 2.13e+03 +evm.model.Chr4.7694 mrna.AA190590.t1 84.84 1886 274 3 136 2012 1 1883 0 2.05e+03 +evm.model.Chr4.7694 mrna.AA064730.t1 82.23 1773 309 1 325 2091 247 2019 0 1.8e+03 +evm.model.Chr4.7694 mrna.AA553910.t1 76.69 2115 469 3 1 2091 1 2115 0 1.75e+03 +evm.model.Chr4.7694 mrna.AA475530.t1 77.63 1967 428 3 13 1970 13 1976 0 1.69e+03 +evm.model.Chr4.7694 mrna.AA449400.t1 79.05 1785 362 1 228 2012 108 1880 0 1.63e+03 +evm.model.Chr4.7694 mrna.AA228980.t1 77.06 1552 320 3 458 1997 344 1871 0 1.3e+03 +evm.model.Chr4.7694 mrna.AA072710.t1 77.83 1376 293 1 638 2013 407 1770 0 1.2e+03 +evm.model.Chr4.7694 mrna.AA279230.t1 90.88 921 84 0 1 921 1 921 0 1.19e+03 +evm.model.Chr4.7694 mrna.AA190610.t1 86.88 1014 130 1 1091 2101 1274 2287 0 1.17e+03 +evm.model.Chr4.7694 mrna.AA190610.t2 86.88 1014 130 1 1091 2101 959 1972 0 1.17e+03 +evm.model.Chr4.7694 mrna.AA190600.t1 88.32 873 102 0 220 1092 295 1167 1.3e-308 1.06e+03 +evm.model.Chr4.7694 mrna.AA171390.t1 74.93 1380 325 3 721 2091 670 2037 1.2e-307 1.06e+03 +evm.model.Chr4.7694 mrna.AA190610.t2 91.60 702 59 0 220 921 259 960 4.7e-268 925 +evm.model.Chr4.7694 mrna.AA190610.t1 91.88 591 48 0 220 810 259 849 1.3e-225 784 +evm.model.Chr4.7694 mrna.AA475530.t1 73.30 1086 281 2 1015 2091 2926 4011 3.5e-224 780 +evm.model.Chr4.7694 mrna.AA078690.t1 73.03 1068 273 3 943 2007 853 1908 3.6e-214 746 +evm.model.Chr4.7694 mrna.AA171390.t1 81.92 636 115 0 1 636 1 636 3.6e-183 644 +evm.model.Chr4.7694 mrna.AA443850.t1 82.52 635 102 2 1387 2012 127 761 7.7e-180 632 +evm.model.Chr4.7694 mrna.AA078690.t1 83.14 522 76 1 17 526 17 538 3.1e-151 538 +evm.model.Chr4.7694 mrna.AA475530.t1 79.88 497 100 0 522 1018 2364 2860 3.2e-131 471 +evm.model.Chr4.7694 mrna.AA072710.t1 85.40 404 59 0 172 575 4 407 5.6e-126 454 +evm.model.Chr4.7694 mrna.AA190600.t1 81.74 438 71 2 1584 2012 1614 2051 1.7e-115 419 +evm.model.Chr4.7694 mrna.AA190600.t1 78.93 413 87 0 1090 1502 1201 1613 1.4e-103 379 +evm.model.Chr4.7694 mrna.AA190610.t1 91.30 230 20 0 692 921 1046 1275 3.2e-80 302 +evm.model.Chr4.7694 mrna.AA190600.t1 87.33 221 28 0 1 221 1 221 2.6e-68 262 +evm.model.Chr4.7694 mrna.AA175170.t1 88.54 192 22 0 424 615 508 699 3.3e-60 236 +evm.model.Chr4.7694 mrna.AA190610.t1 90.11 182 18 0 523 704 847 1028 3e-59 232 +evm.model.Chr4.7694 mrna.AA064730.t1 82.57 218 38 0 4 221 25 242 2.4e-57 226 +evm.model.Chr4.7694 mrna.AA175170.t1 82.57 218 38 0 4 221 52 269 2.4e-57 226 +evm.model.Chr4.7694 mrna.AA185610.t1 85.07 201 30 0 789 989 201 401 7.2e-57 225 +evm.model.Chr4.7694 mrna.AA551600.t1 81.11 217 41 0 4 220 217 433 5.2e-54 215 +evm.model.Chr4.7694 mrna.AA228980.t1 86.93 176 23 0 220 395 166 341 1.2e-51 207 +evm.model.Chr4.7694 mrna.AA175170.t1 88.54 157 18 0 226 382 352 508 2.4e-47 193 +evm.model.Chr4.7694 mrna.AA190610.t1 86.71 158 21 0 1 158 1 158 5.9e-45 185 +evm.model.Chr4.7694 mrna.AA190610.t2 86.71 158 21 0 1 158 1 158 5.9e-45 185 +evm.model.Chr4.7694 mrna.AA175170.t1 84.81 158 24 0 785 942 698 855 4.2e-42 176 +evm.model.Chr4.7694 mrna.AA222200.t1 85.80 162 20 1 60 221 285 443 1.3e-41 174 +evm.model.Chr4.7694 mrna.AA078690.t1 71.38 283 48 2 571 853 535 784 1.1e-40 171 +evm.model.Chr4.7694 mrna.AA091190.t1 79.58 191 33 1 637 827 550 734 3.4e-40 169 +evm.model.Chr4.7694 mrna.AA091190.t1 88.97 136 15 0 324 459 273 408 3.4e-40 169 +evm.model.Chr4.7694 mrna.AA004430.t1 87.77 139 17 0 323 461 422 560 1e-39 168 +evm.model.Chr4.7694 mrna.AA045610.t1 83.77 154 25 0 789 942 654 807 3.1e-39 166 +evm.model.Chr4.7694 mrna.AA228980.t1 83.23 155 26 0 1 155 1 155 9.2e-39 164 +evm.model.Chr4.7694 mrna.AA210310.t1 81.40 172 29 1 153 324 534 702 8.2e-38 161 +evm.model.Chr4.7694 mrna.AA560130.t1 83.02 159 20 1 1861 2012 30 188 2.2e-36 157 +evm.model.Chr4.7694 mrna.AA496700.t1 78.26 184 23 1 55 221 216 399 6.6e-36 155 +evm.model.Chr4.7694 mrna.AA091190.t1 82.76 145 25 0 11 155 89 233 5.9e-35 152 +evm.model.Chr4.7694 mrna.AA020460.t1 83.45 139 17 1 323 461 260 392 1.2e-30 138 +evm.model.Chr4.7694 mrna.AA333230.t1 85.37 123 17 1 124 246 61 182 8.4e-28 128 +evm.model.Chr4.7694 mrna.AA045610.t1 82.09 134 23 1 22 155 454 586 2.5e-27 126 +evm.model.Chr4.7694 mrna.AA115590.t1 80.62 129 25 0 199 327 679 807 2.5e-27 126 +evm.model.Chr4.7694 mrna.AA378910.t1 80.62 129 25 0 199 327 583 711 2.5e-27 126 +evm.model.Chr4.7694 mrna.AA449400.t1 83.02 106 18 0 47 152 1 106 4.9e-23 112 +evm.model.Chr4.7694 mrna.AA626260.t1 84.85 99 15 0 60 158 696 794 1.5e-22 111 +evm.model.Chr4.7694 mrna.AA091190.t1 89.29 84 9 0 524 607 407 490 3.9e-21 106 +evm.model.Chr4.7694 mrna.AA602150.t1 83.96 106 14 1 220 325 31 133 1.2e-20 104 +evm.model.Chr4.7694 mrna.AA475530.t1 81.44 97 18 0 1995 2091 1977 2073 9.4e-19 98 +evm.model.Chr4.7694 mrna.AA419180.t1 77.78 108 24 0 1888 1995 1303 1410 2.8e-18 96.4 +evm.model.Chr4.7694 mrna.AA455040.t1 77.78 108 24 0 1891 1998 244 351 2.8e-18 96.4 +evm.model.Chr4.7694 mrna.AA045610.t1 87.18 78 10 0 318 395 579 656 2.5e-17 93.3 +evm.model.Chr4.7694 mrna.AA385820.t1 78.57 98 21 0 1 98 106 203 2.3e-16 90.1 +evm.model.Chr4.7694 mrna.AA257650.t1 85.71 77 11 0 931 1007 115 191 6.8e-16 88.5 +evm.model.Chr4.7694 mrna.AA333230.t1 90.91 66 6 0 396 461 312 377 2e-15 87 +evm.model.Chr4.7694 mrna.AA004430.t1 88.24 68 8 0 154 221 259 326 1.8e-14 83.8 +evm.model.Chr4.7694 mrna.AA350740.t1 89.39 66 7 0 396 461 670 735 1.8e-14 83.8 +evm.model.Chr4.7694 mrna.AA316050.t1 85.29 68 10 0 91 158 727 794 1.5e-12 77.5 +evm.model.Chr4.7694 mrna.AA592060.t1 83.82 68 11 0 154 221 235 302 1.3e-11 74.3 +evm.model.Chr4.7694 mrna.AA114100.t1 82.81 64 11 0 1645 1708 867 930 1.1e-09 68 +evm.model.Chr4.7694 mrna.AA384030.t1 87.04 54 7 0 407 460 8 61 9.6e-09 64.8 +evm.model.Chr4.7694 mrna.AA197210.t1 82.86 70 10 1 323 392 1423 1490 2.9e-08 63.2 +evm.model.Chr4.7694 mrna.AA604660.t1 82.86 70 10 1 323 392 244 311 2.9e-08 63.2 +evm.model.Chr4.7694 mrna.AA175730.t1 87.76 49 6 0 645 693 672 720 2.6e-07 60.1 +evm.model.Chr4.7694 mrna.AA078690.t1 84.62 52 8 0 920 971 782 833 7.7e-07 58.5 +evm.model.Chr4.7127 mrna.AA565190.t1 86.78 1036 137 0 1 1036 1 1036 0 1.21e+03 +evm.model.Chr4.7127 mrna.AA118170.t1 70.88 625 182 0 410 1034 461 1085 1.5e-114 414 +evm.model.Chr4.7127 mrna.AA118170.t1 68.78 237 71 1 103 336 124 360 4.2e-29 131 +evm.model.Chr4.3572 mrna.AA563680.t1 82.55 1983 343 1 1 1983 271 2250 0 2.03e+03 +evm.model.Chr4.3572 mrna.AA039440.t1 69.82 908 268 1 1076 1983 1073 1974 5.9e-158 560 +evm.model.Chr4.3572 mrna.AA456020.t1 69.71 908 269 1 1076 1983 959 1860 5.3e-157 557 +evm.model.Chr4.3572 mrna.AA456020.t2 69.71 908 269 1 1076 1983 1073 1974 5.3e-157 557 +evm.model.Chr4.3572 mrna.AA456020.t1 77.14 455 104 0 1 455 1 455 2e-107 392 +evm.model.Chr4.3572 mrna.AA456020.t2 77.14 455 104 0 1 455 115 569 2e-107 392 +evm.model.Chr4.3572 mrna.AA039440.t1 75.60 455 111 0 1 455 115 569 9.3e-101 370 +evm.model.Chr4.3572 mrna.AA039440.t1 66.38 470 125 2 481 950 571 1007 2e-56 223 +evm.model.Chr4.3572 mrna.AA456020.t1 65.96 470 127 2 481 950 457 893 1.6e-54 217 +evm.model.Chr4.3572 mrna.AA456020.t2 65.96 470 127 2 481 950 571 1007 1.6e-54 217 +evm.model.Chr4.5645 mrna.AA559640.t1 59.68 310 125 0 1088 1397 1076 1385 2.3e-18 96.4 +evm.model.Chr4.5406 mrna.AA559640.t1 60.85 281 110 0 1249 1529 1090 1370 8.6e-19 98 +evm.model.Chr4.5406 mrna.AA559640.t1 69.14 81 25 0 1012 1092 880 960 0.00017 50.6 +evm.model.Chr4.1442 mrna.AA563690.t1 76.62 77 18 0 2499 2575 750 826 4.6e-09 66.4 +evm.model.Chr4.7439.1 mrna.AA563690.t1 77.97 59 13 0 694 752 766 824 1.1e-05 53.8 +evm.model.Chr5.2889 mrna.AA564650.t1 56.01 291 128 0 922 1212 991 1281 1.5e-06 56.9 +evm.model.Chr5.1086 mrna.AA559640.t1 62.30 305 115 0 1213 1517 1081 1385 1.8e-25 120 +evm.model.Chr5.1086 mrna.AA559640.t1 63.19 144 53 0 249 392 186 329 7.8e-08 61.7 +evm.model.Chr5.5360 mrna.AA563690.t1 76.67 360 84 0 624 983 498 857 3.4e-81 305 +evm.model.Chr5.5360 mrna.AA563690.t1 75.13 193 48 0 990 1182 888 1080 6.3e-36 155 +evm.model.Chr5.5360 mrna.AA563690.t1 74.29 210 51 1 293 499 206 415 5.6e-35 152 +evm.model.Chr5.651 mrna.AA563690.t1 65.62 96 33 0 1980 2075 723 818 0.00062 49 +evm.model.Chr5.6513 mrna.AA559650.t1 73.13 67 18 0 614 680 608 674 7.6e-05 50.6 +evm.model.Chr5.3939 mrna.AA563690.t1 67.62 105 34 0 942 1046 753 857 3e-07 60.1 +evm.model.Chr5.950 mrna.AA563690.t1 63.47 386 135 2 475 860 478 857 7.3e-33 144 +evm.model.Chr5.950 mrna.AA563690.t1 61.22 196 76 0 164 359 209 404 6.3e-11 71.1 +evm.model.Chr5.2857 mrna.AA559650.t1 61.71 222 79 2 447 665 468 686 3.4e-08 61.7 +evm.model.Chr5.2498 mrna.AA559640.t1 59.53 299 121 0 1111 1409 1087 1385 6.2e-17 91.7 +evm.model.Chr5.2498 mrna.AA559640.t1 56.59 417 181 0 87 503 57 473 5.5e-16 88.5 +evm.model.Chr5.1470 mrna.AA563690.t1 62.18 386 140 2 470 855 485 864 4.3e-28 128 +evm.model.Chr5.1075 mrna.AA559640.t1 62.30 305 115 0 1210 1514 1081 1385 1.8e-25 120 +evm.model.Chr5.1075 mrna.AA559640.t1 63.19 144 53 0 249 392 186 329 7.8e-08 61.7 +evm.model.Chr5.2470 mrna.AA559640.t1 77.58 852 191 0 230 1081 566 1417 4.7e-214 745 +evm.model.Chr5.2470 mrna.AA559640.t1 78.02 232 51 0 1 232 274 505 8e-52 207 +evm.model.Chr5.2470 mrna.AA559640.t1 66.96 339 88 2 1123 1455 1438 1758 5.3e-38 161 +evm.model.Chr5.1428 mrna.AA559640.t1 63.03 211 78 0 188 398 155 365 5.4e-16 88.5 +evm.model.Chr5.3062 mrna.AA560110.t1 53.43 1080 500 1 688 1767 811 1887 1.1e-21 108 +evm.model.Chr5.6647 mrna.AA564650.t1 58.90 163 67 0 712 874 1033 1195 0.0021 47.4 +evm.model.Chr5.3063 mrna.AA560110.t1 53.49 903 417 1 682 1584 811 1710 1.9e-16 90.1 +evm.model.Chr5.3811.1 mrna.AA563690.t1 68.69 99 31 0 799 897 766 864 1.3e-07 60.1 +evm.model.Chr5.2471 mrna.AA559630.t1 83.45 145 24 0 1 145 277 421 1e-36 155 +evm.model.Chr5.2471 mrna.AA559630.t1 65.60 125 40 1 268 389 553 677 1.3e-05 52.2 +evm.model.Chr5.3790 mrna.AA563690.t1 66.99 103 34 0 778 880 754 856 1.2e-06 56.9 +evm.model.Chr5.3790 mrna.AA563690.t1 70.42 71 21 0 529 599 508 578 0.00086 47.4 +evm.model.Chr5.722 mrna.AA564640.t1 70.13 77 23 0 250 326 235 311 0.00013 50.6 +evm.model.Chr6.1990 mrna.AA564640.t1 71.26 87 25 0 1087 1173 226 312 3e-07 60.1 +evm.model.Chr6.6822 mrna.AA563690.t1 57.49 327 136 1 1195 1521 502 825 9.4e-10 68 +evm.model.Chr6.4326 mrna.AA565170.t1 74.50 149 37 1 214 67 1432 1580 1.6e-22 106 +evm.model.Chr6.6091 mrna.AA564640.t1 58.62 261 105 1 33 290 39 299 2e-08 61.7 +evm.model.Chr6.4633_evm.model.Chr6.4634 mrna.AA563300.t1 73.55 828 204 2 59 871 14 841 2.1e-169 596 +evm.model.Chr6.4633_evm.model.Chr6.4634 mrna.AA563300.t1 83.69 141 23 0 1020 1160 1059 1199 3e-35 152 +evm.model.Chr6.6088 mrna.AA564640.t1 57.47 261 111 0 33 293 39 299 6.7e-09 63.2 +evm.model.Chr6.6487 mrna.AA560120.t1 81.58 76 14 0 50 125 842 917 1.6e-13 77.5 +evm.model.Chr6.4839 mrna.AA563690.t1 71.01 69 20 0 1509 1577 498 566 0.0017 47.4 +evm.model.Chr6.6639.2 mrna.AA563690.t1 64.14 396 134 3 617 1011 476 864 3.2e-33 145 +evm.model.Chr6.5198 mrna.AA564640.t1 81.97 61 11 0 8 68 257 317 1e-08 63.2 +evm.model.Chr6.5198 mrna.AA564640.t1 77.61 67 15 0 10 76 235 301 9e-08 60.1 +evm.model.Chr6.5198 mrna.AA564640.t1 80.00 65 10 1 13 77 226 287 2.2e-05 52.2 +evm.model.Chr6.4733 mrna.AA560120.t1 83.29 694 116 0 648 1341 669 1362 2.5e-210 732 +evm.model.Chr6.4733 mrna.AA560120.t1 83.80 605 98 0 31 635 25 629 5.3e-185 648 +evm.model.Chr6.5177 mrna.AA559640.t1 60.51 157 62 0 211 367 184 340 1.6e-05 53.8 +evm.model.Chr6.6782 mrna.AA559640.t1 60.67 300 118 0 1198 1497 1087 1386 3e-20 103 +evm.model.Chr6.4630 mrna.AA563320.t1 77.29 894 203 0 1 894 1 894 1.3e-225 773 +evm.model.Chr7.1417 mrna.AA563690.t1 57.87 356 144 1 512 867 503 852 2.5e-13 79.1 +evm.model.Chr7.1417 mrna.AA563690.t1 62.72 169 63 0 879 1047 888 1056 1.8e-10 69.6 +evm.model.Chr7.1423 mrna.AA563690.t1 62.72 169 63 0 852 1020 888 1056 1.8e-10 69.6 +evm.model.Chr7.1423 mrna.AA563690.t1 63.23 155 57 0 512 666 503 657 1.6e-09 66.4 +evm.model.Chr7.5996 mrna.AA560110.t1 56.32 1037 429 4 772 1802 721 1739 8.4e-39 164 +evm.model.Chr7.5765 mrna.AA560110.t1 62.16 555 210 0 80 634 59 613 1.9e-54 215 +evm.model.Chr7.5765 mrna.AA560110.t1 70.21 188 53 1 685 869 694 881 5.9e-23 111 +evm.model.Chr7.3266 mrna.AA560110.t1 60.32 252 85 1 669 920 801 1037 3.3e-11 72.7 +evm.model.Chr7.6906 mrna.AA560120.t1 72.55 1304 346 2 148 1448 46 1340 9.3e-264 909 +evm.model.Chr7.1841 mrna.AA559650.t1 61.79 123 47 0 580 702 739 861 0.00066 47.4 +evm.model.Chr8.1993.3 mrna.AA559640.t1 59.67 300 121 0 1318 1617 1087 1386 2.4e-17 93.3 +evm.model.Chr8.1993.3 mrna.AA559640.t1 61.54 221 85 0 278 498 101 321 5.2e-14 82.2 +evm.model.Chr8.485 mrna.AA564650.t1 55.56 261 116 0 640 900 1087 1347 0.0019 47.4 +evm.model.Chr8.1511 mrna.AA563690.t1 66.43 143 48 0 209 351 722 864 1.2e-12 75.9 +evm.model.Chr8.6220 mrna.AA563690.t1 74.24 66 17 0 1441 1506 760 825 5e-05 52.2 +evm.model.Chr8.6692 mrna.AA559640.t1 62.50 312 117 0 1177 1488 1087 1398 6.6e-27 125 +evm.model.Chr8.6094 mrna.AA563690.t1 61.97 142 54 0 732 873 723 864 3.4e-06 55.3 +evm.model.Chr8.5187 mrna.AA563690.t1 68.54 89 28 0 928 1016 754 842 2.5e-05 53.8 +evm.model.Chr8.718 mrna.AA563690.t1 64.97 177 62 0 948 1124 888 1064 3.7e-15 85.4 +evm.model.Chr8.6101_evm.model.Chr8.6102 mrna.AA563690.t1 61.27 142 55 0 1770 1911 723 864 6.2e-05 52.2 +evm.model.Chr8.6246 mrna.AA559640.t1 58.75 320 126 1 77 396 50 363 3.9e-13 79.1 +evm.model.Chr9.452 mrna.AA560110.t1 69.88 1849 551 2 71 1916 59 1904 0 1.14e+03 +evm.model.Chr9.1509 mrna.AA560110.t1 85.08 1890 276 1 134 2017 17 1906 0 2.09e+03 +evm.model.Chr9.3003 mrna.AA563690.t1 77.78 63 14 0 1353 1415 747 809 1.8e-06 56.9 +evm.model.Chr9.5675 mrna.AA559640.t1 62.39 117 44 0 6 122 186 302 0.00013 47.4 +evm.model.Chr9.5810 mrna.AA559630.t1 80.00 215 42 1 78 291 605 819 1.9e-49 194 +evm.model.Chr9.5810 mrna.AA559630.t1 74.04 104 10 1 1 87 319 422 3.6e-11 69.6 +evm.model.Chr9.6149 mrna.AA564640.t1 63.10 187 63 2 10 190 115 301 2.6e-07 56.9 +evm.model.Chr9.2676.1 mrna.AA559640.t1 61.40 285 110 0 1239 1523 1089 1373 1.1e-20 104 +evm.model.Chr9.2676.1 mrna.AA559640.t1 56.69 314 136 0 124 437 46 359 9.6e-10 68 +evm.model.Chr9.2676.1 mrna.AA559640.t1 61.71 175 64 1 972 1143 828 1002 6.2e-06 55.3 +evm.model.Chr9.6096 mrna.AA559630.t1 91.10 146 13 0 1 146 277 422 1.3e-47 191 +evm.model.Chr9.6096 mrna.AA559630.t1 81.88 160 29 0 137 296 605 764 5.2e-39 163 +evm.model.Chr9.6524 mrna.AA560110.t1 63.98 236 85 0 1564 1799 1504 1739 3.6e-21 106 +evm.model.Chr9.8048 mrna.AA563690.t1 62.68 142 53 0 855 996 723 864 4.2e-07 58.5 +evm.model.Chr9.2964 mrna.AA560110.t1 60.08 243 82 1 668 910 806 1033 8.9e-10 68 +evm.model.Chr9.5839 mrna.AA563690.t1 60.61 165 65 0 2104 2268 502 666 2.9e-06 56.9 +evm.model.Chr9.6976 mrna.AA564650.t1 55.37 298 133 0 889 1186 1012 1309 6.7e-05 52.2 +evm.model.Chr9.2517 mrna.AA559640.t1 61.72 290 111 0 1180 1469 1096 1385 3.8e-22 109 +evm.model.Chr9.2517 mrna.AA559640.t1 54.95 455 199 1 55 509 25 473 7.5e-08 61.7 +evm.model.Chr9.506 mrna.AA560110.t1 57.38 1037 418 4 778 1808 721 1739 2.8e-49 199 diff --git a/tests/compara/synteny.py/references/test_empty_blocks.lifted.anchors b/tests/compara/synteny.py/references/test_empty_blocks.lifted.anchors new file mode 100644 index 00000000..1d37d6aa --- /dev/null +++ b/tests/compara/synteny.py/references/test_empty_blocks.lifted.anchors @@ -0,0 +1,16 @@ +### +evm.model.Chr4.5631 mrna.AA559650.t1 919 +evm.model.Chr4.5633 mrna.AA559640.t1 1600 +evm.model.Chr4.5634 mrna.AA559630.t1 571 +### +evm.model.Chr4.1717 mrna.AA564650.t1 1210 +evm.model.Chr4.1718.1 mrna.AA564640.t1 389 +### +evm.model.Chr4.7543 mrna.AA563300.t1 356 +evm.model.Chr4.7546 mrna.AA563320.t1 639 +### +evm.model.Chr4.3572 mrna.AA563680.t1 2030 +evm.model.Chr4.3580 mrna.AA563690.t1 411 +### +evm.model.Chr4.7127 mrna.AA565190.t1 1210 +evm.model.Chr4.7128 mrna.AA565170.t1 1580 diff --git a/tests/compara/synteny.py/tests.yml b/tests/compara/synteny.py/tests.yml index 57d1989f..5fea4f84 100644 --- a/tests/compara/synteny.py/tests.yml +++ b/tests/compara/synteny.py/tests.yml @@ -11,3 +11,10 @@ depth: args: __DIR__/inputs/testtigs.testchr.anchors outputs: [] references: [] + +liftover: + action: liftover + opts: --qbed=__DIR__/inputs/test_empty_blocks.a.bed --sbed=__DIR__/inputs/test_empty_blocks.b.bed + args: __DIR__/inputs/test_empty_blocks.last __DIR__/inputs/test_empty_blocks.anchors + outputs: [__DIR__/inputs/test_empty_blocks.lifted.anchors] + references: [references/test_empty_blocks.lifted.anchors]