[ensembl-dev] inconsistencies in version 99 release
Hiram Clawson
hiram at soe.ucsc.edu
Mon Mar 9 16:50:17 GMT 2020
Good Morning Ensembl team:
I have worked my way though processing the recent version 99 release.
I have a set of systematic potential errors I would like to call to
your attention. The good news is that 203 of the species predictions
had no errors at all. On the other hand, I'm having trouble with 63
of the species predictions. Perhaps there is something I am unaware
of that is a good reason for this behavior. Let me know if I'm
making some kind of mistake here.
All of the difficulty falls into the same class of error, the gene
predictions run off the end of the sequence. Perhaps this could be
true on chromosome MT on that circular sequence, but most of these
appear to be on other sequences.
*Question*: Will I find gene definitions that wrap around on the
circular chromosome MT ?
This class of error could easily be checked in the GTF file given
the sequence sizes of the assembly. However, our procedure here is
more extensive than that to catch other potential errors. We convert
the GTF file into the UCSC genePred format with the 'kent'
command: gtfToGenePred with the following options:
gtfToGenePred -geneNameAsName2 -genePredExt -includeVersion \
-infoOut="${infoOut}" "${gtfFile}" stdout | gzip -c > "${genePred}"
The resulting genePred file is then run through the command 'genePredCheck'
which verifies a number of properties of the gene definitions:
genePredCheck -chromSizes="${sizes}" "${genePred}"
The "${sizes}" file is produced from the 'toplevel' fa.gz file, for example:
Haplochromis_burtoni.AstBur1.0.dna.toplevel.fa.gz
With the 'kent' command:
faSize -detailed "${faGz}" | sort -k2,2nr > chrom.sizes
(the sort is optional, it is merely convenient to have them in order by size)
An example error, from the Haplochromis_burtoni.AstBur1.0.99.gtf.gz
file says:
ENSHBUT00000021147.1 txEnd 1204 >= chromSize 1190
The definition lines in the gtf file do indeed have these coordinates:
$ zgrep ENSHBUT00000021147 *.gtf.gz
AFNZ01068173.1 ensembl transcript 1109 1204 . - . gene_id
"ENSHBUG00000015206"; gene_version "1"; transcript_id "ENSHBUT00000021147"; transcript_version
"1"; gene_name "5S_rRNA"; gene_source "ensembl"; gene_biotype "rRNA"; transcript_name
"5S_rRNA-201"; transcript_source "ensembl"; transcript_biotype "rRNA";
AFNZ01068173.1 ensembl exon 1109 1204 . - . gene_id
"ENSHBUG00000015206"; gene_version "1"; transcript_id "ENSHBUT00000021147"; transcript_version
"1"; exon_number "1"; gene_name "5S_rRNA"; gene_source "ensembl"; gene_biotype "rRNA";
transcript_name "5S_rRNA-201"; transcript_source "ensembl"; transcript_biotype "rRNA"; exon_id
"ENSHBUE00000077260"; exon_version "1";
And 1190 is the size of the AFNZ01068173.1 sequence.
Included below is a listing of all the errors I am finding. A sample of five are listed,
if there are that many, and if there are more than 5, I list all of the gene names which
have errors.
Thank you for your kind attention,
--Hiram
#################################################################################################
005 errors Acanthochromis_polyacanthus.ASM210954v1 samples:
# ENSAPOT00000029990.1 txEnd 215322 >= chromSize 215318
# ENSAPOT00000000623.1 txEnd 8176 >= chromSize 8175
# ENSAPOT00000026614.1 txEnd 880 >= chromSize 878
# ENSAPOT00000026495.1 txEnd 819 >= chromSize 817
# ENSAPOT00000026498.1 txEnd 825 >= chromSize 816
001 errors Anas_platyrhynchos_platyrhynchos.CAU_duck1.0 samples:
# ENSAPLT00000028821.1 txEnd 2802 >= chromSize 2775
004 errors Aotus_nancymaae.Anan_2.0 samples:
# ENSANAT00000008002.1 txEnd 21157 >= chromSize 21156
# ENSANAT00000018995.1 txEnd 11710 >= chromSize 11706
# ENSANAT00000001044.1 txEnd 9860 >= chromSize 9850
# ENSANAT00000005144.1 txEnd 3639 >= chromSize 3636
001 errors Apteryx_rowi.aptRow1 samples:
# ENSARWT00000006857.1 txEnd 3698446 >= chromSize 3698432
001 errors Astyanax_mexicanus.Astyanax_mexicanus-2.0 samples:
# ENSAMXT00000033487.1 txEnd 18847 >= chromSize 18840
063 errors Bison_bison_bison.Bison_UMD1.0 samples:
# ENSBBBT00000000224.1 txEnd 5098 >= chromSize 5095
# ENSBBBT00000027836.1 txEnd 1098 >= chromSize 1095
# ENSBBBT00000033534.1 txEnd 892 >= chromSize 884
# ENSBBBT00000028452.1 txEnd 819 >= chromSize 813
# ENSBBBT00000029322.1 txEnd 720 >= chromSize 702
# complete list of errors in Bison_bison_bison.Bison_UMD1.0:
# ENSBBBT00000000224.1 ENSBBBT00000027836.1 ENSBBBT00000033534.1
# ENSBBBT00000028452.1 ENSBBBT00000029322.1 ENSBBBT00000029020.1
# ENSBBBT00000029205.1 ENSBBBT00000029599.1 ENSBBBT00000029015.1
# ENSBBBT00000028160.1 ENSBBBT00000029182.1 ENSBBBT00000029024.1
# ENSBBBT00000029570.1 ENSBBBT00000033586.1 ENSBBBT00000027682.1
# ENSBBBT00000028562.1 ENSBBBT00000028963.1 ENSBBBT00000033862.1
# ENSBBBT00000033948.1 ENSBBBT00000028627.1 ENSBBBT00000027410.1
# ENSBBBT00000028941.1 ENSBBBT00000033092.1 ENSBBBT00000033782.1
# ENSBBBT00000033195.1 ENSBBBT00000028097.1 ENSBBBT00000027392.1
# ENSBBBT00000033370.1 ENSBBBT00000030127.1 ENSBBBT00000029947.1
# ENSBBBT00000017232.1 ENSBBBT00000017404.1 ENSBBBT00000016486.1
# ENSBBBT00000017667.1 ENSBBBT00000028597.1 ENSBBBT00000029793.1
# ENSBBBT00000033523.1 ENSBBBT00000029564.1 ENSBBBT00000033424.1
# ENSBBBT00000027988.1 ENSBBBT00000027855.1 ENSBBBT00000017441.1
# ENSBBBT00000029497.1 ENSBBBT00000028451.1 ENSBBBT00000028940.1
# ENSBBBT00000016665.1 ENSBBBT00000017571.1 ENSBBBT00000033556.1
# ENSBBBT00000033264.1 ENSBBBT00000017686.1 ENSBBBT00000033747.1
# ENSBBBT00000017216.1 ENSBBBT00000028675.1 ENSBBBT00000029917.1
# ENSBBBT00000033930.1 ENSBBBT00000030004.1 ENSBBBT00000017696.1
# ENSBBBT00000030093.1 ENSBBBT00000028463.1 ENSBBBT00000027872.1
# ENSBBBT00000027944.1 ENSBBBT00000028154.1 ENSBBBT00000017339.1
004 errors Calidris_pygmaea.ASM369795v1 samples:
# ENSCPGT00000006906.1 txEnd 3003 >= chromSize 2978
# ENSCPGT00000018677.1 txEnd 1428 >= chromSize 1403
# ENSCPGT00000028815.1 txEnd 1020 >= chromSize 1011
# ENSCPGT00000013522.1 txEnd 987 >= chromSize 983
001 errors Canis_lupus_dingo.ASM325472v1 samples:
# ENSCAFT00020024070.1 txEnd 43905 >= chromSize 43897
004 errors Carlito_syrichta.Tarsius_syrichta-2.0.1 samples:
# ENSTSYT00000036298.1 txEnd 9974 >= chromSize 9960
# ENSTSYT00000025862.1 txEnd 865 >= chromSize 863
# ENSTSYT00000041648.1 txEnd 480 >= chromSize 479
# ENSTSYT00000046606.1 txEnd 454 >= chromSize 452
005 errors Castor_canadensis.C.can_genome_v1.0 samples:
# ENSCCNT00000035766.1 txEnd 399274 >= chromSize 399238
# ENSCCNT00000020851.1 txEnd 142739 >= chromSize 142735
# ENSCCNT00000009989.1 txEnd 44219 >= chromSize 44200
# ENSCCNT00000023094.1 txEnd 41900 >= chromSize 41897
# ENSCCNT00000029367.1 txEnd 16780 >= chromSize 16778
002 errors Chrysemys_picta_bellii.Chrysemys_picta_bellii-3.0.3 samples:
# ENSCPBT00000005691.1 txEnd 766 >= chromSize 727
# ENSCPBT00000006187.1 txEnd 614 >= chromSize 603
005 errors Cricetulus_griseus_crigri.CriGri_1.0 samples:
# ENSCGRT00000030264.1 txEnd 1987 >= chromSize 1967
# ENSCGRT00000031181.1 txEnd 539 >= chromSize 538
# ENSCGRT00000030473.1 txEnd 377 >= chromSize 360
# ENSCGRT00000027739.1 txEnd 252 >= chromSize 243
# ENSCGRT00000027716.1 txEnd 256 >= chromSize 231
004 errors Cyanistes_caeruleus.cyaCae2 samples:
# ENSCCET00000009649.1 txEnd 22913 >= chromSize 22908
# ENSCCET00000005359.1 txEnd 10599 >= chromSize 10594
# ENSCCET00000004984.1 txEnd 2025 >= chromSize 2002
# ENSCCET00000000934.1 txEnd 1463 >= chromSize 1452
002 errors Cynoglossus_semilaevis.Cse_v1.0 samples:
# ENSCSET00000012881.1 txEnd 221 >= chromSize 218
# ENSCSET00000012889.1 txEnd 217 >= chromSize 211
003 errors Dipodomys_ordii.Dord_2.0 samples:
# ENSDORT00000021579.2 txEnd 43903 >= chromSize 43893
# ENSDORT00000020465.2 txEnd 13704 >= chromSize 13697
# ENSDORT00000034132.1 txEnd 1251 >= chromSize 1244
002 errors Fukomys_damarensis.DMR_v1.0 samples:
# ENSFDAT00000001669.1 txEnd 301 >= chromSize 295
# ENSFDAT00000026393.1 txEnd 223 >= chromSize 221
007 errors Gopherus_agassizii.ASM289641v1 samples:
# ENSGAGT00000024361.1 txEnd 143482 >= chromSize 143480
# ENSGAGT00000007527.1 txEnd 11973 >= chromSize 11949
# ENSGAGT00000004574.1 txEnd 621 >= chromSize 617
# ENSGAGT00000004859.1 txEnd 436 >= chromSize 424
# ENSGAGT00000004877.1 txEnd 413 >= chromSize 412
# complete list of errors in Gopherus_agassizii.ASM289641v1:
# ENSGAGT00000024361.1 ENSGAGT00000007527.1 ENSGAGT00000004574.1
# ENSGAGT00000004859.1 ENSGAGT00000004877.1 ENSGAGT00000004982.1
# ENSGAGT00000005103.1
007 errors Gorilla_gorilla.gorGor4 samples:
# ENSGGOT00000040833.2 txEnd 2008 >= chromSize 2000
# ENSGGOT00000066834.1 txEnd 2009 >= chromSize 2000
# ENSGGOT00000065889.1 txEnd 1325 >= chromSize 1322
# ENSGGOT00000041741.2 txEnd 923 >= chromSize 913
# ENSGGOT00000064312.1 txEnd 900 >= chromSize 894
# complete list of errors in Gorilla_gorilla.gorGor4:
# ENSGGOT00000040833.2 ENSGGOT00000066834.1 ENSGGOT00000065889.1
# ENSGGOT00000041741.2 ENSGGOT00000064312.1 ENSGGOT00000042831.1
# ENSGGOT00000039360.2
001 errors Haplochromis_burtoni.AstBur1.0 samples:
# ENSHBUT00000021147.1 txEnd 1204 >= chromSize 1190
004 errors Heterocephalus_glaber_male.HetGla_1.0 samples:
# ENSHGLT00100030844.1 txEnd 1131 >= chromSize 1114
# ENSHGLT00100031497.1 txEnd 799 >= chromSize 726
# ENSHGLT00100031744.1 txEnd 433 >= chromSize 421
# ENSHGLT00100029130.1 txEnd 261 >= chromSize 258
001 errors Hippocampus_comes.H_comes_QL1_v1 samples:
# ENSHCOT00000000413.1 txEnd 261 >= chromSize 245
002 errors Hucho_hucho.ASM331708v1 samples:
# ENSHHUT00000082792.1 txEnd 102045 >= chromSize 102019
# ENSHHUT00000032536.1 txEnd 70503 >= chromSize 70494
002 errors Ictalurus_punctatus.IpCoco_1.2 samples:
# ENSIPUT00000001753.1 txEnd 1094 >= chromSize 1078
# ENSIPUT00000002346.1 txEnd 701 >= chromSize 698
002 errors Jaculus_jaculus.JacJac1.0 samples:
# ENSJJAT00000007476.1 txEnd 4410 >= chromSize 4389
# ENSJJAT00000002946.1 txEnd 1935 >= chromSize 1923
001 errors Kryptolebias_marmoratus.ASM164957v1 samples:
# ENSKMAT00000019077.1 txEnd 104390 >= chromSize 104380
004 errors Labrus_bergylta.BallGen_V1 samples:
# ENSLBET00000009719.1 txEnd 22497 >= chromSize 22474
# ENSLBET00000007818.1 txEnd 13707 >= chromSize 13706
# ENSLBET00000003994.1 txEnd 11940 >= chromSize 11935
# ENSLBET00000015176.1 txEnd 3232 >= chromSize 3227
006 errors Lates_calcarifer.ASB_HGAPassembly_v1 samples:
# ENSLCAT00010023934.1 txEnd 1379921 >= chromSize 1379868
# ENSLCAT00010051454.1 txEnd 25148 >= chromSize 25142
# ENSLCAT00010000909.1 txEnd 22945 >= chromSize 22935
# ENSLCAT00010015983.1 txEnd 20096 >= chromSize 20085
# ENSLCAT00010055260.1 txEnd 19184 >= chromSize 19171
# complete list of errors in Lates_calcarifer.ASB_HGAPassembly_v1:
# ENSLCAT00010023934.1 ENSLCAT00010051454.1 ENSLCAT00010000909.1
# ENSLCAT00010015983.1 ENSLCAT00010055260.1 ENSLCAT00010034120.1
001 errors Macaca_fascicularis.Macaca_fascicularis_5.0 samples:
# ENSMFAT00000049321.1 txEnd 5011 >= chromSize 5009
001 errors Mandrillus_leucophaeus.Mleu.le_1.0 samples:
# ENSMLET00000030838.1 txEnd 35289 >= chromSize 35264
001 errors Marmota_marmota_marmota.marMar2.1 samples:
# ENSMMMT00000002271.1 txEnd 2301 >= chromSize 2297
005 errors Meriones_unguiculatus.MunDraft-v1.0 samples:
# ENSMUGT00000024940.1 txEnd 131998 >= chromSize 131993
# ENSMUGT00000008130.1 txEnd 28915 >= chromSize 28897
# ENSMUGT00000006800.1 txEnd 2559 >= chromSize 2552
# ENSMUGT00000007576.1 txEnd 2124 >= chromSize 2106
# ENSMUGT00000002146.1 txEnd 1509 >= chromSize 1477
002 errors Mesocricetus_auratus.MesAur1.0 samples:
# ENSMAUT00000008954.1 txEnd 18377 >= chromSize 18369
# ENSMAUT00000008838.1 txEnd 1152 >= chromSize 1150
006 errors Microcebus_murinus.Mmur_3.0 samples:
# ENSMICT00000068593.1 txEnd 5528 >= chromSize 5525
# ENSMICT00000068583.1 txEnd 4860 >= chromSize 4858
# ENSMICT00000039077.2 txEnd 4792 >= chromSize 4790
# ENSMICT00000052172.2 txEnd 2742 >= chromSize 2739
# ENSMICT00000049755.2 txEnd 1553 >= chromSize 1539
# complete list of errors in Microcebus_murinus.Mmur_3.0:
# ENSMICT00000068593.1 ENSMICT00000068583.1 ENSMICT00000039077.2
# ENSMICT00000052172.2 ENSMICT00000049755.2 ENSMICT00000068718.1
001 errors Monopterus_albus.M_albus_1.0 samples:
# ENSMALT00000009433.1 txEnd 463 >= chromSize 458
010 errors Nannospalax_galili.S.galili_v1.0 samples:
# ENSNGAT00000010911.1 txEnd 1279026 >= chromSize 1279023
# ENSNGAT00000011043.1 txEnd 3095 >= chromSize 3068
# ENSNGAT00000005613.1 txEnd 883 >= chromSize 874
# ENSNGAT00000005469.1 txEnd 843 >= chromSize 822
# ENSNGAT00000003195.1 txEnd 661 >= chromSize 657
# complete list of errors in Nannospalax_galili.S.galili_v1.0:
# ENSNGAT00000010911.1 ENSNGAT00000011043.1 ENSNGAT00000005613.1
# ENSNGAT00000005469.1 ENSNGAT00000003195.1 ENSNGAT00000004333.1
# ENSNGAT00000010598.1 ENSNGAT00000004053.1 ENSNGAT00000004795.1
# ENSNGAT00000008686.1
001 errors Octodon_degus.OctDeg1.0 samples:
# ENSODET00000030480.1 txEnd 10465 >= chromSize 10456
002 errors Ornithorhynchus_anatinus.OANA5 samples:
# ENSOANT00000006034.3 txEnd 11788 >= chromSize 11786
# ENSOANT00000008951.2 txEnd 557 >= chromSize 556
001 errors Pan_paniscus.panpan1.1 samples:
# ENSPPAT00000007687.1 txEnd 2172 >= chromSize 2168
003 errors Pan_troglodytes.Pan_tro_3.0 samples:
# ENSPTRT00000103531.1 txEnd 10764 >= chromSize 10756
# ENSPTRT00000079867.1 txEnd 1416 >= chromSize 1400
# ENSPTRT00000096982.1 txEnd 1326 >= chromSize 1310
002 errors Panthera_pardus.PanPar1.0 samples:
# ENSPPRT00000027040.1 txEnd 3387 >= chromSize 3385
# ENSPPRT00000025676.1 txEnd 382 >= chromSize 377
001 errors Papio_anubis.Panu_3.0 samples:
# ENSPANT00000043361.1 txEnd 1439 >= chromSize 1433
001 errors Paramormyrops_kingsleyae.PKINGS_0.1 samples:
# ENSPKIT00000040233.1 txEnd 985 >= chromSize 979
003 errors Piliocolobus_tephrosceles.ASM277652v2 samples:
# ENSPTET00000004864.1 txEnd 4295 >= chromSize 4264
# ENSPTET00000012530.1 txEnd 1686 >= chromSize 1655
# ENSPTET00000012977.1 txEnd 420 >= chromSize 416
001 errors Poecilia_latipinna.P_latipinna-1.0 samples:
# ENSPLAT00000006289.1 txEnd 106993 >= chromSize 106985
001 errors Poecilia_reticulata.Guppy_female_1.0_MT samples:
# ENSPRET00000010679.1 txEnd 1748 >= chromSize 1723
007 errors Pogona_vitticeps.pvi1.1 samples:
# ENSPVIT00000007700.1 txEnd 1359 >= chromSize 1356
# ENSPVIT00000000869.1 txEnd 195 >= chromSize 194
# ENSPVIT00000000758.1 txEnd 148 >= chromSize 147
# ENSPVIT00000000674.1 txEnd 136 >= chromSize 134
# ENSPVIT00000000663.1 txEnd 131 >= chromSize 130
# complete list of errors in Pogona_vitticeps.pvi1.1:
# ENSPVIT00000007700.1 ENSPVIT00000000869.1 ENSPVIT00000000758.1
# ENSPVIT00000000674.1 ENSPVIT00000000663.1 ENSPVIT00000000651.1
# ENSPVIT00000000610.1
007 errors Prolemur_simus.Prosim_1.0 samples:
# ENSPSMT00000004661.1 txEnd 1913 >= chromSize 1912
# ENSPSMT00000003255.1 txEnd 997 >= chromSize 991
# ENSPSMT00000003068.1 txEnd 881 >= chromSize 879
# ENSPSMT00000002350.1 txEnd 597 >= chromSize 592
# ENSPSMT00000002266.1 txEnd 585 >= chromSize 580
# complete list of errors in Prolemur_simus.Prosim_1.0:
# ENSPSMT00000004661.1 ENSPSMT00000003255.1 ENSPSMT00000003068.1
# ENSPSMT00000002350.1 ENSPSMT00000002266.1 ENSPSMT00000001781.1
# ENSPSMT00000001734.1
001 errors Propithecus_coquereli.Pcoq_1.0 samples:
# ENSPCOT00000008378.1 txEnd 14532 >= chromSize 14529
119 errors Pygocentrus_nattereri.Pygocentrus_nattereri-1.0.2 samples:
# ENSPNAT00000030325.1 txEnd 787 >= chromSize 786
# ENSPNAT00000026753.1 txEnd 649 >= chromSize 635
# ENSPNAT00000030091.1 txEnd 573 >= chromSize 571
# ENSPNAT00000039693.1 txEnd 574 >= chromSize 567
# ENSPNAT00000030039.1 txEnd 562 >= chromSize 551
# complete list of errors in Pygocentrus_nattereri.Pygocentrus_nattereri-1.0.2:
# ENSPNAT00000030325.1 ENSPNAT00000026753.1 ENSPNAT00000030091.1
# ENSPNAT00000039693.1 ENSPNAT00000030039.1 ENSPNAT00000029569.1
# ENSPNAT00000029493.1 ENSPNAT00000029279.1 ENSPNAT00000029228.1
# ENSPNAT00000029109.1 ENSPNAT00000029033.1 ENSPNAT00000028242.1
# ENSPNAT00000034320.1 ENSPNAT00000033869.1 ENSPNAT00000033585.1
# ENSPNAT00000033252.1 ENSPNAT00000032816.1 ENSPNAT00000040560.1
# ENSPNAT00000032623.1 ENSPNAT00000040532.1 ENSPNAT00000032458.1
# ENSPNAT00000032313.1 ENSPNAT00000040419.1 ENSPNAT00000040304.1
# ENSPNAT00000031921.1 ENSPNAT00000031833.1 ENSPNAT00000031822.1
# ENSPNAT00000031766.1 ENSPNAT00000040129.1 ENSPNAT00000031124.1
# ENSPNAT00000031115.1 ENSPNAT00000034273.1 ENSPNAT00000034255.1
# ENSPNAT00000034259.1 ENSPNAT00000041084.1 ENSPNAT00000041007.1
# ENSPNAT00000033971.1 ENSPNAT00000033943.1 ENSPNAT00000033868.1
# ENSPNAT00000033797.1 ENSPNAT00000033776.1 ENSPNAT00000040886.1
# ENSPNAT00000033708.1 ENSPNAT00000040861.1 ENSPNAT00000033430.1
# ENSPNAT00000040753.1 ENSPNAT00000033324.1 ENSPNAT00000033261.1
# ENSPNAT00000040718.1 ENSPNAT00000033202.1 ENSPNAT00000033177.1
# ENSPNAT00000040653.1 ENSPNAT00000032873.1 ENSPNAT00000032731.1
# ENSPNAT00000032697.1 ENSPNAT00000032426.1 ENSPNAT00000031460.1
# ENSPNAT00000040135.1 ENSPNAT00000040021.1 ENSPNAT00000030954.1
# ENSPNAT00000030758.1 ENSPNAT00000030373.1 ENSPNAT00000039773.1
# ENSPNAT00000029875.1 ENSPNAT00000039583.1 ENSPNAT00000039575.1
# ENSPNAT00000029528.1 ENSPNAT00000029506.1 ENSPNAT00000029341.1
# ENSPNAT00000029198.1 ENSPNAT00000029063.1 ENSPNAT00000039341.1
# ENSPNAT00000028815.1 ENSPNAT00000028678.1 ENSPNAT00000028681.1
# ENSPNAT00000039123.1 ENSPNAT00000028137.1 ENSPNAT00000028120.1
# ENSPNAT00000039095.1 ENSPNAT00000039098.1 ENSPNAT00000034407.1
# ENSPNAT00000041135.1 ENSPNAT00000034260.1 ENSPNAT00000034059.1
# ENSPNAT00000034049.1 ENSPNAT00000041000.1 ENSPNAT00000034020.1
# ENSPNAT00000040977.1 ENSPNAT00000033970.1 ENSPNAT00000033887.1
# ENSPNAT00000033709.1 ENSPNAT00000033543.1 ENSPNAT00000033429.1
# ENSPNAT00000033381.1 ENSPNAT00000033276.1 ENSPNAT00000033269.1
# ENSPNAT00000033054.1 ENSPNAT00000032992.1 ENSPNAT00000032987.1
# ENSPNAT00000032959.1 ENSPNAT00000040591.1 ENSPNAT00000032620.1
# ENSPNAT00000040524.1 ENSPNAT00000040480.1 ENSPNAT00000032347.1
# ENSPNAT00000032367.1 ENSPNAT00000032283.1 ENSPNAT00000032273.1
# ENSPNAT00000032113.1 ENSPNAT00000031787.1 ENSPNAT00000039943.1
# ENSPNAT00000030668.1 ENSPNAT00000030436.1 ENSPNAT00000039846.1
# ENSPNAT00000030407.1 ENSPNAT00000030416.1 ENSPNAT00000030418.1
# ENSPNAT00000030424.1 ENSPNAT00000030426.1
005 errors Rhinopithecus_bieti.ASM169854v1 samples:
# ENSRBIT00000004729.1 txEnd 1295 >= chromSize 1287
# ENSRBIT00000004240.1 txEnd 925 >= chromSize 896
# ENSRBIT00000007958.1 txEnd 874 >= chromSize 870
# ENSRBIT00000005433.1 txEnd 499 >= chromSize 496
# ENSRBIT00000004757.1 txEnd 492 >= chromSize 474
009 errors Rhinopithecus_roxellana.Rrox_v1 samples:
# ENSRROT00000015658.1 txEnd 2904 >= chromSize 2895
# ENSRROT00000003328.1 txEnd 575 >= chromSize 551
# ENSRROT00000003014.1 txEnd 553 >= chromSize 550
# ENSRROT00000017963.1 txEnd 425 >= chromSize 423
# ENSRROT00000004422.1 txEnd 409 >= chromSize 406
# complete list of errors in Rhinopithecus_roxellana.Rrox_v1:
# ENSRROT00000015658.1 ENSRROT00000003328.1 ENSRROT00000003014.1
# ENSRROT00000017963.1 ENSRROT00000004422.1 ENSRROT00000005493.1
# ENSRROT00000010204.1 ENSRROT00000009486.1 ENSRROT00000000177.1
001 errors Saimiri_boliviensis_boliviensis.SaiBol1.0 samples:
# ENSSBOT00000006176.1 txEnd 1192 >= chromSize 1189
001 errors Serinus_canaria.SCA1 samples:
# ENSSCAT00000001915.1 txEnd 371 >= chromSize 370
004 errors Seriola_dumerili.Sdu_1.0 samples:
# ENSSDUT00000013268.1 txEnd 1149 >= chromSize 1143
# ENSSDUT00000005753.1 txEnd 211 >= chromSize 206
# ENSSDUT00000014103.1 txEnd 193 >= chromSize 192
# ENSSDUT00000013010.1 txEnd 111 >= chromSize 107
012 errors Seriola_lalandi_dorsalis.Sedor1 samples:
# ENSSLDT00000007605.1 txEnd 1027 >= chromSize 1011
# ENSSLDT00000010043.1 txEnd 672 >= chromSize 642
# ENSSLDT00000003900.1 txEnd 588 >= chromSize 571
# ENSSLDT00000009742.1 txEnd 572 >= chromSize 567
# ENSSLDT00000003943.1 txEnd 578 >= chromSize 565
# complete list of errors in Seriola_lalandi_dorsalis.Sedor1:
# ENSSLDT00000007605.1 ENSSLDT00000010043.1 ENSSLDT00000003900.1
# ENSSLDT00000009742.1 ENSSLDT00000003943.1 ENSSLDT00000013254.1
# ENSSLDT00000014154.1 ENSSLDT00000013370.1 ENSSLDT00000014372.1
# ENSSLDT00000010767.1 ENSSLDT00000014836.1 ENSSLDT00000015182.1
007 errors Sinocyclocheilus_anshuiensis.SAMN03320099.WGS_v1.1 samples:
# ENSSANT00000006639.1 txEnd 1376 >= chromSize 1372
# ENSSANT00000042011.1 txEnd 1060 >= chromSize 1048
# ENSSANT00000048660.1 txEnd 781 >= chromSize 774
# ENSSANT00000036030.1 txEnd 653 >= chromSize 650
# ENSSANT00000035713.1 txEnd 409 >= chromSize 406
# complete list of errors in Sinocyclocheilus_anshuiensis.SAMN03320099.WGS_v1.1:
# ENSSANT00000006639.1 ENSSANT00000042011.1 ENSSANT00000048660.1
# ENSSANT00000036030.1 ENSSANT00000035713.1 ENSSANT00000035604.1
# ENSSANT00000035571.1
002 errors Sinocyclocheilus_grahami.SAMN03320097.WGS_v1.1 samples:
# ENSSGRT00000007067.1 txEnd 2581 >= chromSize 2579
# ENSSGRT00000007167.1 txEnd 522 >= chromSize 511
016 errors Sinocyclocheilus_rhinocerous.SAMN03320098_v1.1 samples:
# ENSSRHT00000019549.1 txEnd 1295 >= chromSize 1285
# ENSSRHT00000065396.1 txEnd 1215 >= chromSize 1214
# ENSSRHT00000008712.1 txEnd 789 >= chromSize 787
# ENSSRHT00000019577.1 txEnd 585 >= chromSize 579
# ENSSRHT00000064870.1 txEnd 546 >= chromSize 545
# complete list of errors in Sinocyclocheilus_rhinocerous.SAMN03320098_v1.1:
# ENSSRHT00000019549.1 ENSSRHT00000065396.1 ENSSRHT00000008712.1
# ENSSRHT00000019577.1 ENSSRHT00000064870.1 ENSSRHT00000034204.1
# ENSSRHT00000078111.1 ENSSRHT00000099515.1 ENSSRHT00000009482.1
# ENSSRHT00000010774.1 ENSSRHT00000010743.1 ENSSRHT00000010736.1
# ENSSRHT00000010732.1 ENSSRHT00000010719.1 ENSSRHT00000010716.1
# ENSSRHT00000010704.1
011 errors Spermophilus_dauricus.ASM240643v1 samples:
# ENSSDAT00000016599.1 txEnd 11632 >= chromSize 11604
# ENSSDAT00000019251.1 txEnd 1445 >= chromSize 1443
# ENSSDAT00000020016.1 txEnd 844 >= chromSize 824
# ENSSDAT00000020034.1 txEnd 812 >= chromSize 804
# ENSSDAT00000020173.1 txEnd 695 >= chromSize 679
# complete list of errors in Spermophilus_dauricus.ASM240643v1:
# ENSSDAT00000016599.1 ENSSDAT00000019251.1 ENSSDAT00000020016.1
# ENSSDAT00000020034.1 ENSSDAT00000020173.1 ENSSDAT00000020300.1
# ENSSDAT00000020406.1 ENSSDAT00000020446.1 ENSSDAT00000020530.1
# ENSSDAT00000020597.1 ENSSDAT00000020678.1
001 errors Sus_scrofa_usmarc.USMARCv1.0 samples:
# ENSSSCT00070007926.1 txEnd 15013 >= chromSize 14986
001 errors Urocitellus_parryii.ASM342692v1 samples:
# ENSUPAT00010012239.1 txEnd 4507 >= chromSize 4504
001 errors Ursus_americanus.ASM334442v1 samples:
# ENSUAMT00000003375.1 txEnd 4630 >= chromSize 4622
001 errors Ursus_maritimus.UrsMar_1.0 samples:
# ENSUMAT00000000039.1 txEnd 262 >= chromSize 259
#################################################################################################
No errors found in:
#################################################################################################
Accipiter_nisus.Accipiter_nisus_ver1.0
Ailuropoda_melanoleuca.ailMel1
Amazona_collaria.ASM394721v1
Amphilophus_citrinellus.Midas_v5
Amphiprion_ocellaris.AmpOce1.0
Amphiprion_percula.Nemo_v1
Anabas_testudineus.fAnaTes1.1
Anolis_carolinensis.AnoCar2.0
Anser_brachyrhynchus.ASM259213v1
Anser_cygnoides.GooseV1.0
Apteryx_haastii.aptHaa1
Apteryx_owenii.aptOwe1
Aquila_chrysaetos_chrysaetos.bAquChr1.2
Astatotilapia_calliptera.fAstCal1.2
Astyanax_mexicanus_pachon.Astyanax_mexicanus-1.0.2
Athene_cunicularia.athCun1
Betta_splendens.fBetSpl5.2
Bos_grunniens.LU_Bosgru_v3.0
Bos_indicus_hybrid.UOA_Brahman_1
Bos_mutus.BosGru_v2.0
Bos_taurus.ARS-UCD1.2
Bos_taurus_hybrid.UOA_Angus_1
Caenorhabditis_elegans.WBcel235
Calidris_pugnax.ASM143184v1
Callithrix_jacchus.ASM275486v1
Callorhinchus_milii.Callorhinchus_milii-6.1.3
Camelus_dromedarius.CamDro2
Canis_familiaris.CanFam3.1
Canis_lupus_familiarisbasenji.Basenji_breed-1.1
Canis_lupus_familiarisgreatdane.UMICH_Zoey_3.1
Capra_hircus.ARS1
Catagonus_wagneri.CatWag_v2_BIUU_UCD
Cavia_aperea.CavAp1.0
Cavia_porcellus.Cavpor3.0
Cebus_capucinus.Cebus_imitator-1.0
Cercocebus_atys.Caty_1.0
Chelonoidis_abingdonii.ASM359739v1
Chinchilla_lanigera.ChiLan1.0
Chlorocebus_sabaeus.ChlSab1.1
Choloepus_hoffmanni.choHof1
Chrysolophus_pictus.Chrysolophus_pictus_GenomeV1.0
Ciona_intestinalis.KH
Ciona_savignyi.CSAV2.0
Clupea_harengus.Ch_v2.0.2
Colobus_angolensis_palliatus.Cang.pa_1.0
Cottoperca_gobio.fCotGob3.1
Coturnix_japonica.Coturnix_japonica_2.0
Cricetulus_griseus_chok1gshd.CHOK1GS_HDv1
Cricetulus_griseus_picr.CriGri-PICR
Crocodylus_porosus.CroPor_comp1
Cyprinodon_variegatus.C_variegatus-1.0
Cyprinus_carpio_germanmirror.German_Mirror_carp_1.0
Cyprinus_carpio_hebaored.Hebao_red_carp_1.0
Cyprinus_carpio_huanghe.Hunaghe_carp_2.0
Danio_rerio.GRCz11
Dasypus_novemcinctus.Dasnov3.0
Denticeps_clupeoides.fDenClu1.1
Dromaius_novaehollandiae.droNov1
Drosophila_melanogaster.BDGP6.28
Echeneis_naucrates.fEcheNa1.1
Echinops_telfairi.TENREC
Electrophorus_electricus.Ee_SOAP_WITH_SSPACE
Eptatretus_burgeri.Eburgeri_3.2
Equus_asinus_asinus.ASM303372v1
Equus_caballus.EquCab3.0
Erinaceus_europaeus.HEDGEHOG
Erpetoichthys_calabaricus.fErpCal1.1
Erythrura_gouldiae.GouldianFinch
Esox_lucius.Eluc_V3
Felis_catus.Felis_catus_9.0
Ficedula_albicollis.FicAlb_1.4
Fundulus_heteroclitus.Fundulus_heteroclitus-3.0.2
Gadus_morhua.gadMor1
Gallus_gallus.GRCg6a
Gambusia_affinis.ASM309773v1
Gasterosteus_aculeatus.BROADS1
Gouania_willdenowi.fGouWil2.1
Heterocephalus_glaber_female.HetGla_female_1.0
Homo_sapiens.GRCh38
Ictidomys_tridecemlineatus.SpeTri2.0
Junco_hyemalis.ASM382977v1
Larimichthys_crocea.L_crocea_2.0
Latimeria_chalumnae.LatCha1
Lepidothrix_coronata.Lepidothrix_coronata-1.0
Lepisosteus_oculatus.LepOcu1
Lonchura_striata_domestica.LonStrDom1
Loxodonta_africana.loxAfr3
Lynx_canadensis.mLynCan4_v1.p
Macaca_mulatta.Mmul_10
Macaca_nemestrina.Mnem_1.0
Manacus_vitellinus.ASM171598v2
Mastacembelus_armatus.fMasArm1.1
Maylandia_zebra.M_zebra_UMD2a
Meleagris_gallopavo.Turkey_2.01
Melopsittacus_undulatus.Melopsittacus_undulatus_6.3
Microtus_ochrogaster.MicOch1.0
Mola_mola.ASM169857v1
Monodelphis_domestica.ASM229v1
Moschus_moschiferus.MosMos_v2_BIUU_UCD
Mus_caroli.CAROLI_EIJ_v1.1
Mus_musculus.GRCm38
Mus_musculus_129s1svimj.129S1_SvImJ_v1
Mus_musculus_aj.A_J_v1
Mus_musculus_akrj.AKR_J_v1
Mus_musculus_balbcj.BALB_cJ_v1
Mus_musculus_c3hhej.C3H_HeJ_v1
Mus_musculus_c57bl6nj.C57BL_6NJ_v1
Mus_musculus_casteij.CAST_EiJ_v1
Mus_musculus_cbaj.CBA_J_v1
Mus_musculus_dba2j.DBA_2J_v1
Mus_musculus_fvbnj.FVB_NJ_v1
Mus_musculus_lpj.LP_J_v1
Mus_musculus_nodshiltj.NOD_ShiLtJ_v1
Mus_musculus_nzohlltj.NZO_HlLtJ_v1
Mus_musculus_pwkphj.PWK_PhJ_v1
Mus_musculus_wsbeij.WSB_EiJ_v1
Mus_pahari.PAHARI_EIJ_v1.1
Mus_spicilegus.MUSP714
Mus_spretus.SPRET_EiJ_v1
Mustela_putorius_furo.MusPutFur1.0
Myotis_lucifugus.Myoluc2.0
Myripristis_murdjan.fMyrMur1.1
Neogobius_melanostomus.RGoby_Basel_V2
Neolamprologus_brichardi.NeoBri1.0
Neovison_vison.NNQGG.v01
Nomascus_leucogenys.Nleu_3.0
Notamacropus_eugenii.Meug_1.0
Notechis_scutatus.TS10Xv2-PRI
Nothoprocta_perdicaria.notPer1
Numida_meleagris.NumMel1.0
Ochotona_princeps.OchPri2.0-Ens
Oreochromis_aureus.ASM587006v1
Oreochromis_niloticus.O_niloticus_UMD_NMBU
Oryctolagus_cuniculus.OryCun2.0
Oryzias_latipes.ASM223467v1
Oryzias_latipes_hni.ASM223471v1
Oryzias_latipes_hsok.ASM223469v1
Oryzias_melastigma.Om_v0.7.RACA
Otolemur_garnettii.OtoGar3
Ovis_aries.Oar_v3.1
Panthera_tigris_altaica.PanTig1.0
Parambassis_ranga.fParRan2.1
Parus_major.Parus_major1.1
Pavo_cristatus.AIIM_Pcri_1.0
Pelodiscus_sinensis.PelSin_1.0
Periophthalmus_magnuspinnatus.PM.fa
Peromyscus_maniculatus_bairdii.HU_Pman_2.1
Petromyzon_marinus.Pmarinus_7.0
Phascolarctos_cinereus.phaCin_unsw_v4.1
Phasianus_colchicus.ASM414374v1
Physeter_catodon.ASM283717v2
Podarcis_muralis.PodMur_1.0
Poecilia_formosa.PoeFor_5.1.2
Poecilia_mexicana.P_mexicana-1.0
Pongo_abelii.PPYG2
Procavia_capensis.proCap1
Pseudonaja_textilis.EBS10Xv2-PRI
Pteropus_vampyrus.pteVam1
Pundamilia_nyererei.PunNye1.0
Rhinolophus_ferrumequinum.mRhiFer1_v1.p
Saccharomyces_cerevisiae.R64-1-1
Salarias_fasciatus.fSalaFa1.1
Salmo_salar.ICSASG_v2
Salmo_trutta.fSalTru1.1
Salvator_merianae.HLtupMer3
Sarcophilus_harrisii.DEVIL7.0
Scleropages_formosus.fSclFor1.1
Scophthalmus_maximus.ASM318616v1
Sorex_araneus.COMMON_SHREW1
Sparus_aurata.fSpaAur1.1
Sphaeramia_orbicularis.fSphaOr1.1
Sphenodon_punctatus.ASM311381v1
Stegastes_partitus.Stegastes_partitus-1.0.2
Strigops_habroptila.bStrHab1_v1.p
Struthio_camelus_australis.ASM69896v1
Suricata_suricatta.meerkat_22Aug2017_6uvM2_HiC
Sus_scrofa.Sscrofa11.1
Sus_scrofa_bamei.Bamei_pig_v1
Sus_scrofa_berkshire.Berkshire_pig_v1
Sus_scrofa_hampshire.Hampshire_pig_v1
Sus_scrofa_jinhua.Jinhua_pig_v1
Sus_scrofa_landrace.Landrace_pig_v1
Sus_scrofa_largewhite.Large_White_v1
Sus_scrofa_meishan.Meishan_pig_v1
Sus_scrofa_pietrain.Pietrain_pig_v1
Sus_scrofa_rongchang.Rongchang_pig_v1
Sus_scrofa_tibetan.Tibetan_Pig_v2
Sus_scrofa_wuzhishan.minipig_v1.0
Taeniopygia_guttata.bTaeGut1_v1.p
Takifugu_rubripes.fTakRub1.2
Terrapene_carolina_triunguis.T_m_triunguis-2.0
Tetraodon_nigroviridis.TETRAODON8
Theropithecus_gelada.Tgel_1.0
Tupaia_belangeri.TREESHREW
Tursiops_truncatus.turTru1
Varanus_komodoensis.ASM479886v1
Vicugna_pacos.vicPac1
Vombatus_ursinus.bare-nosed_wombat_genome_assembly
Vulpes_vulpes.VulVul2.2
Xenopus_tropicalis.Xenopus_tropicalis_v9.1
Xiphophorus_couchianus.Xiphophorus_couchianus-4.0.1
Xiphophorus_maculatus.X_maculatus-5.0-male
Zonotrichia_albicollis.Zonotrichia_albicollis-1.0.1
######################################################################################################
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