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@kimrutherford @github-actions
kimrutherford authored and github-actions[bot] committed Dec 22, 2024
1 parent 40ec072 commit fab6207
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Showing 11 changed files with 14,550 additions and 14,540 deletions.
10,852 changes: 5,428 additions & 5,424 deletions data/alleles.tsv
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6 changes: 3 additions & 3 deletions data/chromosome1.contig
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Expand Up @@ -6359,7 +6359,7 @@ FT /controlled_curation="term=species distribution, conserved
FT in bacteria; date=20100820"
FT /db_xref="SPD:17/17D05"
FT /primary_name="aro4"
FT /synomym="aro3"
FT /synonym="aro3"
FT 3'UTR 469827..469890
FT /db_xref="EMBL:AU007393"
FT /systematic_id="SPAC24H6.10c"
Expand Down Expand Up @@ -11001,7 +11001,7 @@ FT CDS complement(join(782142..782336,782438..782704,782803..78314
FT /colour=7
FT /primary_name="atp10"
FT /product="mitochondrial F1-FO ATP synthase chaperone,
FT catalytic core Atp10"
FT Atp10"
FT /systematic_id="SPAC4G8.11c"
FT /db_xref="SPD:14/14G05"
FT /controlled_curation="term=species distribution, conserved
Expand Down Expand Up @@ -80850,7 +80850,7 @@ FT in eukaryotes; date=20100820"
FT /controlled_curation="term=species distribution, conserved
FT in bacteria; date=20100820"
FT /primary_name="aro3"
FT /synontm="aro4"
FT /synonym="aro4"
FT lncRNA 5326840..5328155
FT /db_xref="PMID:29914874"
FT /db_xref="PMID:21511999"
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2 changes: 1 addition & 1 deletion data/chromosome2.contig
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Expand Up @@ -34363,7 +34363,7 @@ FT /db_xref="PMID:21511999"
FT CDS complement(join(2269573..2271274,2271318..2272430,2272511..2272776))
FT /colour=10
FT /product="WD repeat protein, human WDR7 ortholog,
FT implicated vacuolar acidification, autophgy, or vacuole
FT implicated vacuolar acidification, autophagy, or vacuole
FT localization"
FT /db_xref="SPD:48/48A07"
FT /systematic_id="SPBC16H5.13"
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4 changes: 1 addition & 3 deletions data/chromosome3.contig
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Expand Up @@ -26140,7 +26140,7 @@ FT /systematic_id="SPCC297.06c"
FT /db_xref="PMID:21511999"
FT CDS complement(1885962..1886654)
FT /colour=10
FT /product="conserved fungal protein"
FT /product="conserved protein, fungi and plants"
FT /synonym="SPCC737.01c"
FT /db_xref="SPD:08/08B02"
FT /systematic_id="SPCC297.06c"
Expand All @@ -26149,8 +26149,6 @@ FT in fungi; date=20081110"
FT /controlled_curation="term=species distribution,
FT predominantly single copy (one to one); date=20081110"
FT /controlled_curation="term=species distribution, conserved
FT in fungi only; date=20081110"
FT /controlled_curation="term=species distribution, conserved
FT in eukaryotes; date=20080202"
FT 5'UTR complement(1886655..1886868)
FT /systematic_id="SPCC297.06c"
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18 changes: 9 additions & 9 deletions results/allele_auto_fix.tsv
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@@ -1,14 +1,14 @@
systematic_id allele_id allele_name allele_description allele_type change_description_to change_name_to change_type_to auto_fix_comment sequence_error solution_index allele_parts rules_applied reference
SPAC140.02 SPAC140.02:allele-3 gar2::ura4+ gar2::ura4+ disruption gar2::ura4 syntax_error gar2::ura4+ disruption:usual PMID:7596817,PMID:9211982
SPAC18G6.02c SPAC18G6.02c:allele-10 chp1-alpha-mut1 KKRKK71NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KKRKK71NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
SPAC23C4.19 SPAC23C4.19:allele-17 spt5-CTD-T1E(7) 801-990,S800SGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGS amino_acid_insertion_and_mutation amino_acid_insertion_and_deletion type_error 801-990|S800SGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGS partial_amino_acid_deletion:multiple_aa|amino_acid_insertion:standard PMID:32366382
SPAC56E4.04c SPAC56E4.04c:allele-5 cut6-1 L1910S amino_acid_mutation L1877S old_coords_fix, revision 8148: complement(join(1246095..1252807,1253430..1253559)) L1910 L1910S amino_acid_mutation:single_aa PMID:37792890
SPAC977.10 SPAC977.10:allele-59 nhe1-REL6 EIEKSIYE390QSSGNSHIKE amino_acid_mutation amino_acid_insertion_and_mutation type_error EIEKSIYE390QSSGNSHIKE amino_acid_insertion_and_mutation:multiple_aa PMID:30996236
SPBC215.05 SPBC215.05:allele-3 gpd1-G4BS TTACGTCA(-324)CGGAAGACTCTCCTCCG nucleotide_mutation nucleotide_insertion_and_mutation type_error TTACGTCA(-324)CGGAAGACTCTCCTCCG nucleotide_insertion_and_mutation:multiple_nt PMID:25122751
SPBC28F2.12 SPBC28F2.12:allele-16 rpb1-CTD-S2A(r1-r12)delta(r13-r29) CTD-S2A(r1-r12)delta(r13-r29) amino_acid_deletion_and_mutation CTD-S2A(r1-r12),delta(r13-r29) syntax_error CTD-S2A(r1-r12)delta(r13-r29) amino_acid_deletion_and_mutation:CTD PMID:22144909
SPBC28F2.12 SPBC28F2.12:allele-52 rpb1-CTD-S2A(r5-r29)S7A(r5-r29) CTD-S2A(r5-r29)S7A(r5-r29) amino_acid_mutation CTD-S2A(r5-r29),S7A(r5-r29) syntax_error CTD-S2A(r5-r29)S7A(r5-r29) amino_acid_mutation:CTD PMID:22771993
SPBC3H7.13 SPBC3H7.13:allele-7 csc1::ura4+ csc1::ura4+ disruption csc1::ura4 syntax_error csc1::ura4+ disruption:usual PMID:23874188
SPBC428.08c SPBC428.08c:allele-8 clr4-alpha-mut KRRKR58NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KRRKR58NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
SPAC18G6.02c SPAC18G6.02c:allele-23 chp1-alpha-mut1 KKRKK71NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KKRKK71NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
SPAC23C4.19 SPAC23C4.19:allele-24 spt5-CTD-T1E(7) 801-990,S800SGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGS amino_acid_insertion_and_mutation amino_acid_insertion_and_deletion type_error 801-990|S800SGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGSGSKEPAWNSGS partial_amino_acid_deletion:multiple_aa|amino_acid_insertion:standard PMID:32366382
SPAC56E4.04c SPAC56E4.04c:allele-8 cut6-1 L1910S amino_acid_mutation L1877S old_coords_fix, revision 8148: complement(join(1246095..1252807,1253430..1253559)) L1910 L1910S amino_acid_mutation:single_aa PMID:37792890
SPAC977.10 SPAC977.10:allele-108 nhe1-REL6 EIEKSIYE390QSSGNSHIKE amino_acid_mutation amino_acid_insertion_and_mutation type_error EIEKSIYE390QSSGNSHIKE amino_acid_insertion_and_mutation:multiple_aa PMID:30996236
SPBC215.05 SPBC215.05:allele-2 gpd1-G4BS TTACGTCA(-324)CGGAAGACTCTCCTCCG nucleotide_mutation nucleotide_insertion_and_mutation type_error TTACGTCA(-324)CGGAAGACTCTCCTCCG nucleotide_insertion_and_mutation:multiple_nt PMID:25122751
SPBC28F2.12 SPBC28F2.12:allele-21 rpb1-CTD-S2A(r1-r12)delta(r13-r29) CTD-S2A(r1-r12)delta(r13-r29) amino_acid_deletion_and_mutation CTD-S2A(r1-r12),delta(r13-r29) syntax_error CTD-S2A(r1-r12)delta(r13-r29) amino_acid_deletion_and_mutation:CTD PMID:22144909
SPBC28F2.12 SPBC28F2.12:allele-31 rpb1-CTD-S2A(r5-r29)S7A(r5-r29) CTD-S2A(r5-r29)S7A(r5-r29) amino_acid_mutation CTD-S2A(r5-r29),S7A(r5-r29) syntax_error CTD-S2A(r5-r29)S7A(r5-r29) amino_acid_mutation:CTD PMID:22771993
SPBC3H7.13 SPBC3H7.13:allele-2 csc1::ura4+ csc1::ura4+ disruption csc1::ura4 syntax_error csc1::ura4+ disruption:usual PMID:23874188
SPBC428.08c SPBC428.08c:allele-20 clr4-alpha-mut KRRKR58NEHG amino_acid_mutation amino_acid_deletion_and_mutation type_error KRRKR58NEHG amino_acid_deletion_and_mutation:multiple_aa PMID:22727667
SPCC285.07c SPCC285.07c:allele-2 wtf18-2D366NN D366N,D366DN amino_acid_insertion_and_mutation D47N,D47DN multi_shift_fix D366|D366 0 D366N|D366DN amino_acid_mutation:single_aa|amino_acid_insertion:standard PMID:30475921
SPCC285.07c SPCC285.07c:allele-2 wtf18-2D366NN D366N,D366DN amino_acid_insertion_and_mutation D58DN,D58N multi_shift_fix D366|D366 1 D366N|D366DN amino_acid_mutation:single_aa|amino_acid_insertion:standard PMID:30475921
SPCC285.07c SPCC285.07c:allele-2 wtf18-2D366NN D366N,D366DN amino_acid_insertion_and_mutation D79N,D79DN multi_shift_fix D366|D366 2 D366N|D366DN amino_acid_mutation:single_aa|amino_acid_insertion:standard PMID:30475921
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