Table 5.
Counts of fatal VADR alerts reported for the test datasets
| NC | NP | DC | DP | total | ||
|---|---|---|---|---|---|---|
| alert | 1384 seqs | 32190 seqs | 4580 seqs | 20973 seqs | 59127 seqs | |
| code | error message | ct(seqs) | ct(seqs) | ct(seqs) | ct(seqs) | ct(seqs) |
| peptrans | PEPTIDE_TRANSLATION_PROBLEM | 516(86) | 716(535) | 1330(95) | 4051(1065) | 6613(1781) |
| noannotn | NO_ANNOTATION | - | 512(512) | 5(5) | 2236(2236) | 2753(2753) |
| indf3pst | INDEFINITE_ANNOTATION_END | 82(70) | 1059(1029) | 56(56) | 600(593) | 1797(1748) |
| indf5pst | INDEFINITE_ANNOTATION_START | 59(57) | 940(876) | 16(16) | 660(574) | 1675(1523) |
| indf3loc | INDEFINITE_ANNOTATION_END | 85(48) | 185(90) | 206(98) | 293(136) | 769(372) |
| incgroup | INCORRECT_SPECIFIED_GROUP | 19(19) | 302(302) | 30(30) | 286(286) | 637(637) |
| indf5loc | INDEFINITE_ANNOTATION_START | 19(15) | 66(35) | 222(135) | 286(144) | 593(329) |
| lowcovrg | LOW_COVERAGE | 3(3) | 217(217) | 60(60) | 279(279) | 559(559) |
| unexleng | UNEXPECTED_LENGTH | 42(34) | 66(55) | 105(49) | 318(182) | 531(320) |
| indf5gap | INDEFINITE_ANNOTATION_START | 6(3) | 23(12) | 117(100) | 220(127) | 366(242) |
| indf3gap | INDEFINITE_ANNOTATION_END | 4(2) | 83(71) | 15(14) | 237(133) | 339(220) |
| lowsim3f | LOW_FEATURE_SIMILARITY_END | - | - | 272(88) | 20(9) | 292(97) |
| cdsstopp | CDS_HAS_STOP_CODON | 7(5) | 112(111) | 15(15) | 153(153) | 287(284) |
| revcompl | REVCOMPLEM | 3(3) | 85(85) | 35(35) | 120(120) | 243(243) |
| cdsstopn | CDS_HAS_STOP_CODON | 96(93) | 72(71) | 58(58) | 5(4) | 231(226) |
| insertnp | INSERTION_OF_NT | 50(43) | 151(138) | - | 2(2) | 203(183) |
| lowsim5f | LOW_FEATURE_SIMILARITY_START | - | - | 101(101) | 79(39) | 180(140) |
| lowsim3s | LOW_SIMILARITY_END | 61(61) | 80(80) | 2(2) | 5(5) | 148(148) |
| mutstart | MUTATION_AT_START | 13(11) | 58(58) | 8(8) | 35(27) | 114(104) |
| mutendcd | MUTATION_AT_END | 52(50) | 47(46) | 6(6) | 5(4) | 110(106) |
| discontn | DISCONTINUOUS_SIMILARITY | - | 8(8) | 25(25) | 35(35) | 68(68) |
| dupregin | DUPLICATE_REGIONS | - | 6(6) | 33(33) | 25(25) | 64(64) |
| indfstrn | INDEFINITE_STRAND | 1(1) | 4(4) | 56(56) | 2(2) | 63(63) |
| deletinp | DELETION_OF_NT | 22(20) | 26(25) | - | 12(6) | 60(51) |
| lowsimif | LOW_FEATURE_SIMILARITY | - | - | 29(14) | 18(9) | 47(23) |
| indf3plg | INDEFINITE_ANNOTATION_END | 1(1) | 40(40) | - | 2(2) | 43(43) |
| indfantn | INDEFINITE_ANNOTATION | 1(1) | 23(23) | - | 18(17) | 42(41) |
| lowsim5s | LOW_SIMILARITY_START | 12(12) | - | 6(6) | 20(20) | 38(38) |
| noftrann | NO_FEATURES_ANNOTATED | - | 1(1) | - | 26(26) | 27(27) |
| indf5plg | INDEFINITE_ANNOTATION_START | - | 10(10) | - | - | 10(10) |
| indfantp | INDEFINITE_ANNOTATION | - | 3(3) | - | 6(6) | 9(9) |
| pepadjcy | PEPTIDE_ADJACENCY_PROBLEM | - | 3(3) | - | 6(6) | 9(9) |
| mutendex | MUTATION_AT_END | 2(2) | 5(5) | 1(1) | - | 8(8) |
| mutendns | MUTATION_AT_END | 1(1) | 5(5) | - | - | 6(6) |
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