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Table 5 Counts of fatal VADR alerts reported for the test datasets

From: VADR: validation and annotation of virus sequence submissions to GenBank

  NCNPDCDPtotal
alert 1384 seqs32190 seqs4580 seqs20973 seqs59127 seqs
codeerror messagect(seqs)ct(seqs)ct(seqs)ct(seqs)ct(seqs)
peptransPEPTIDE_TRANSLATION_PROBLEM516(86)716(535)1330(95)4051(1065)6613(1781)
noannotnNO_ANNOTATION-512(512)5(5)2236(2236)2753(2753)
indf3pstINDEFINITE_ANNOTATION_END82(70)1059(1029)56(56)600(593)1797(1748)
indf5pstINDEFINITE_ANNOTATION_START59(57)940(876)16(16)660(574)1675(1523)
indf3locINDEFINITE_ANNOTATION_END85(48)185(90)206(98)293(136)769(372)
incgroupINCORRECT_SPECIFIED_GROUP19(19)302(302)30(30)286(286)637(637)
indf5locINDEFINITE_ANNOTATION_START19(15)66(35)222(135)286(144)593(329)
lowcovrgLOW_COVERAGE3(3)217(217)60(60)279(279)559(559)
unexlengUNEXPECTED_LENGTH42(34)66(55)105(49)318(182)531(320)
indf5gapINDEFINITE_ANNOTATION_START6(3)23(12)117(100)220(127)366(242)
indf3gapINDEFINITE_ANNOTATION_END4(2)83(71)15(14)237(133)339(220)
lowsim3fLOW_FEATURE_SIMILARITY_END--272(88)20(9)292(97)
cdsstoppCDS_HAS_STOP_CODON7(5)112(111)15(15)153(153)287(284)
revcomplREVCOMPLEM3(3)85(85)35(35)120(120)243(243)
cdsstopnCDS_HAS_STOP_CODON96(93)72(71)58(58)5(4)231(226)
insertnpINSERTION_OF_NT50(43)151(138)-2(2)203(183)
lowsim5fLOW_FEATURE_SIMILARITY_START--101(101)79(39)180(140)
lowsim3sLOW_SIMILARITY_END61(61)80(80)2(2)5(5)148(148)
mutstartMUTATION_AT_START13(11)58(58)8(8)35(27)114(104)
mutendcdMUTATION_AT_END52(50)47(46)6(6)5(4)110(106)
discontnDISCONTINUOUS_SIMILARITY-8(8)25(25)35(35)68(68)
dupreginDUPLICATE_REGIONS-6(6)33(33)25(25)64(64)
indfstrnINDEFINITE_STRAND1(1)4(4)56(56)2(2)63(63)
deletinpDELETION_OF_NT22(20)26(25)-12(6)60(51)
lowsimifLOW_FEATURE_SIMILARITY--29(14)18(9)47(23)
indf3plgINDEFINITE_ANNOTATION_END1(1)40(40)-2(2)43(43)
indfantnINDEFINITE_ANNOTATION1(1)23(23)-18(17)42(41)
lowsim5sLOW_SIMILARITY_START12(12)-6(6)20(20)38(38)
noftrannNO_FEATURES_ANNOTATED-1(1)-26(26)27(27)
indf5plgINDEFINITE_ANNOTATION_START-10(10)--10(10)
indfantpINDEFINITE_ANNOTATION-3(3)-6(6)9(9)
pepadjcyPEPTIDE_ADJACENCY_PROBLEM-3(3)-6(6)9(9)
mutendexMUTATION_AT_END2(2)5(5)1(1)-8(8)
mutendnsMUTATION_AT_END1(1)5(5)--6(6)
  1. The 34 fatal alert codes reported at least once for any test dataset are listed sorted by total number of reports. 4 fatal alert types (unexdivg, lowsimis, incsbgrp and indfstrp) were not reported for any of the four test sets and are not shown. See Table 3 for more information on alerts