TB-Profiler result

Run: ERR4769551
Summary

Run ID: ERR4769551

Sample name:

Date: 01-04-2023 06:44:16

Number of reads: 374572

Percentage reads mapped: 27.04

Strain: La1.3

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
La1 M.bovis None None 1.0
La1.3 M.bovis None None 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.12 kanamycin, capreomycin, aminoglycosides, amikacin
pncA 2289073 p.His57Asp missense_variant 1.0 pyrazinamide
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 5752 c.513G>A synonymous_variant 1.0
gyrA 6406 c.-896C>T upstream_gene_variant 1.0
gyrB 6446 p.Ala403Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8285 c.984C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761234 c.1428G>C synonymous_variant 0.11
rpoB 761255 c.1449T>G synonymous_variant 0.11
rpoB 761261 c.1455G>C synonymous_variant 0.12
rpoB 761273 c.1467T>C synonymous_variant 0.12
rpoB 761294 c.1488G>C synonymous_variant 0.13
rpoB 761300 c.1494G>C synonymous_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763468 c.99G>C synonymous_variant 0.22
rpoC 763486 c.117T>C synonymous_variant 0.25
rpoC 763492 c.123G>C synonymous_variant 0.25
rpoC 763507 c.138G>C synonymous_variant 0.2
rpoC 764611 c.1242G>C synonymous_variant 0.18
rpoC 764646 p.Gly426Ala missense_variant 0.15
rpoC 764650 c.1281G>T synonymous_variant 0.17
rpoC 764662 c.1293G>C synonymous_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.24
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.12
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.13
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.13
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.32
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.42
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.44
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.12
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.12
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.39
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.11
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.12
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.36
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 0.22
rrs 1472289 n.444T>G non_coding_transcript_exon_variant 0.3
rrs 1472290 n.445C>G non_coding_transcript_exon_variant 0.3
rrs 1472297 n.453_465delGTCCGGGTTCTCT non_coding_transcript_exon_variant 0.25
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.25
rrs 1472324 n.479G>C non_coding_transcript_exon_variant 0.23
rrs 1472325 n.480G>C non_coding_transcript_exon_variant 0.23
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.15
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.25
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.25
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.22
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.4
rrs 1472599 n.754G>A non_coding_transcript_exon_variant 0.38
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.47
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.44
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.5
rrs 1472686 n.841G>A non_coding_transcript_exon_variant 0.44
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.47
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.41
rrs 1472951 n.1106T>C non_coding_transcript_exon_variant 0.25
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.25
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.25
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.25
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.25
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.33
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.17
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.33
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.42
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.2
rrs 1473099 n.1254T>G non_coding_transcript_exon_variant 0.22
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.44
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.4
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.4
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.4
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.22
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.44
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.33
rrs 1473129 n.1284C>T non_coding_transcript_exon_variant 0.18
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.2
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.12
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.47
rrs 1473282 n.1437C>T non_coding_transcript_exon_variant 0.44
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.5
rrl 1473717 n.60G>A non_coding_transcript_exon_variant 0.19
rrl 1473731 n.74T>A non_coding_transcript_exon_variant 0.27
rrl 1473756 n.99G>T non_coding_transcript_exon_variant 0.27
rrl 1473757 n.100T>G non_coding_transcript_exon_variant 0.27
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.27
rrl 1473770 n.113T>G non_coding_transcript_exon_variant 0.29
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.31
rrl 1473814 n.157A>G non_coding_transcript_exon_variant 0.31
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.31
rrl 1473830 n.173T>C non_coding_transcript_exon_variant 0.24
rrl 1473832 n.175C>T non_coding_transcript_exon_variant 0.24
rrl 1473833 n.176_177insT non_coding_transcript_exon_variant 0.24
rrl 1473844 n.187C>T non_coding_transcript_exon_variant 0.24
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.18
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.15
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.25
rrl 1474740 n.1083G>C non_coding_transcript_exon_variant 0.25
rrl 1474747 n.1090C>G non_coding_transcript_exon_variant 0.25
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.22
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.22
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.22
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.29
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.22
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.3
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.27
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.27
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.25
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.25
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.23
rrl 1475443 n.1786G>A non_coding_transcript_exon_variant 0.17
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.17
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.17
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.18
rrl 1475481 n.1824C>T non_coding_transcript_exon_variant 0.2
rrl 1475482 n.1825A>T non_coding_transcript_exon_variant 0.2
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.29
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.18
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.29
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.24
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.28
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.2
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.17
rrl 1476110 n.2453G>T non_coding_transcript_exon_variant 0.12
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.12
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.12
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.12
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.12
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.12
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.15
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.13
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.25
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.22
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.18
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.12
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.12
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.21
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.19
rrl 1476300 n.2643G>A non_coding_transcript_exon_variant 0.18
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.12
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.12
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.18
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.18
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.17
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.17
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.12
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.14
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.14
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.13
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.21
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.16
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.12
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.35
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.11
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.24
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.21
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.2
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.17
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.17
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.19
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.16
rrl 1476614 n.2957A>T non_coding_transcript_exon_variant 0.18
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.2
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.15
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.15
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.15
rrl 1476728 n.3071T>C non_coding_transcript_exon_variant 1.0
rpsA 1833894 p.Ala118Glu missense_variant 0.29
rpsA 1833928 c.387G>C synonymous_variant 0.29
rpsA 1834340 p.Met267Leu missense_variant 0.12
rpsA 1834348 c.807T>C synonymous_variant 0.2
rpsA 1834354 c.813G>C synonymous_variant 0.21
rpsA 1834357 c.816T>C synonymous_variant 0.2
rpsA 1834360 c.819G>C synonymous_variant 0.14
rpsA 1834361 c.820T>C synonymous_variant 0.21
rpsA 1834366 c.825A>G synonymous_variant 0.21
rpsA 1834375 c.834G>A synonymous_variant 0.14
rpsA 1834378 c.837T>G synonymous_variant 0.2
rpsA 1834387 c.846C>T synonymous_variant 0.18
rpsA 1834396 c.855G>T synonymous_variant 0.13
rpsA 1834399 p.His286Gln missense_variant 0.13
rpsA 1834411 c.870T>G synonymous_variant 0.14
rpsA 1834417 c.876G>C synonymous_variant 0.14
rpsA 1834435 c.894G>C synonymous_variant 0.14
rpsA 1834447 c.906C>G synonymous_variant 0.13
rpsA 1834451 c.910T>C synonymous_variant 0.12
rpsA 1834540 c.999G>T synonymous_variant 0.18
rpsA 1834543 c.1002C>G synonymous_variant 0.18
rpsA 1834546 c.1005T>C synonymous_variant 0.2
rpsA 1834552 c.1011G>T synonymous_variant 0.2
rpsA 1834555 c.1014T>C synonymous_variant 0.2
rpsA 1834557 p.Ala339Gly missense_variant 0.2
rpsA 1834570 c.1029C>T synonymous_variant 0.22
rpsA 1834573 c.1032G>A synonymous_variant 0.25
rpsA 1834574 p.Met345Leu missense_variant 0.25
rpsA 1834600 c.1059G>C synonymous_variant 0.22
rpsA 1834606 c.1065C>T synonymous_variant 0.18
rpsA 1834612 c.1071G>T synonymous_variant 0.18
rpsA 1834619 c.1078T>C synonymous_variant 0.17
rpsA 1834627 c.1086C>G synonymous_variant 0.23
rpsA 1834633 c.1092A>G synonymous_variant 0.15
rpsA 1834639 c.1098T>C synonymous_variant 0.14
rpsA 1834645 c.1104C>T synonymous_variant 0.15
rpsA 1834650 p.Thr370Asn missense_variant 0.17
rpsA 1834859 p.Ala440Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102017 c.1026C>T synonymous_variant 0.13
ndh 2103173 c.-132delG upstream_gene_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 1.0
katG 2156025 c.87C>A synonymous_variant 1.0
katG 2156465 c.-354C>T upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168011 p.Ser868Arg missense_variant 1.0
PPE35 2168814 c.1798dupA frameshift_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726636 c.444G>C synonymous_variant 0.22
ahpC 2726638 p.Ala149Val missense_variant 0.22
ahpC 2726642 c.450C>A synonymous_variant 0.2
ahpC 2726651 c.459G>C synonymous_variant 0.22
ahpC 2726654 c.462G>C synonymous_variant 0.22
ahpC 2726657 c.465A>C synonymous_variant 0.18
ahpC 2726660 c.468C>T synonymous_variant 0.18
ahpC 2726669 c.477T>C synonymous_variant 0.17
ahpC 2726675 c.483A>T synonymous_variant 0.17
ahpC 2726678 c.486G>C synonymous_variant 0.15
ahpC 2726681 c.489A>C synonymous_variant 0.18
ahpC 2726684 c.492G>C synonymous_variant 0.18
ahpC 2726693 c.501C>T synonymous_variant 0.18
ahpC 2726700 c.508_509delTCinsAG synonymous_variant 0.18
ald 3086728 c.-92C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474427 p.Val141Ile missense_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4038403 c.2302T>C synonymous_variant 1.0
clpC1 4039382 c.1323C>G synonymous_variant 0.14
clpC1 4039391 c.1314T>G synonymous_variant 0.17
clpC1 4039394 c.1311G>C synonymous_variant 0.17
clpC1 4039397 c.1308A>G synonymous_variant 0.15
clpC1 4039406 c.1299G>C synonymous_variant 0.15
clpC1 4039412 c.1293T>G synonymous_variant 0.15
clpC1 4039415 p.Glu430Asp missense_variant 0.23
clpC1 4039424 p.Lys427Arg missense_variant 0.17
clpC1 4039427 p.Glu426Asp missense_variant 0.17
clpC1 4039430 c.1275T>C synonymous_variant 0.17
clpC1 4039436 c.1269G>A synonymous_variant 0.18
clpC1 4039442 c.1263A>G synonymous_variant 0.18
clpC1 4039448 c.1257A>G synonymous_variant 0.18
clpC1 4039457 c.1248C>T synonymous_variant 0.15
clpC1 4039463 c.1242C>G synonymous_variant 0.15
clpC1 4039469 c.1236T>C synonymous_variant 0.15
clpC1 4039472 c.1233G>C synonymous_variant 0.15
clpC1 4039478 c.1227G>A synonymous_variant 0.18
clpC1 4039481 c.1224T>G synonymous_variant 0.17
clpC1 4039484 c.1221T>C synonymous_variant 0.18
clpC1 4039499 c.1206G>C synonymous_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241384 p.Pro508Thr missense_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242760 c.-473G>A upstream_gene_variant 0.15
embA 4242970 c.-263C>T upstream_gene_variant 1.0
embA 4244220 c.988C>T synonymous_variant 1.0
embB 4246551 p.Asn13Ser missense_variant 1.0
embB 4246864 c.351C>T synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249640 c.3127T>C synonymous_variant 0.23
aftB 4267858 p.Ile327Val missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0