TB-Profiler result

Run: SRR19303773
Summary

Run ID: SRR19303773

Sample name:

Date: 03-04-2023 21:06:03

Number of reads: 466509

Percentage reads mapped: 15.28

Strain: lineage4.6.2.2

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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 0.44 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.3 kanamycin, capreomycin, aminoglycosides, amikacin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7395 p.Ala32Thr missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7704 p.Thr135Ser missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.18
mshA 576104 p.Arg253Gly missense_variant 0.4
mshA 576113 p.Arg256Gly missense_variant 0.33
rpoC 762989 c.-381G>C upstream_gene_variant 0.12
rpoC 762995 c.-375G>T upstream_gene_variant 0.11
rpoB 763014 p.Met1070Leu missense_variant 0.11
rpoC 763028 c.-342T>C upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 0.11
rpoC 763034 c.-336C>G upstream_gene_variant 0.12
rpoB 763038 p.Thr1078Ala missense_variant 0.12
rpoC 763052 c.-318G>C upstream_gene_variant 0.11
rpoC 763053 c.-317T>C upstream_gene_variant 0.11
rpoC 763094 c.-276G>C upstream_gene_variant 0.11
rpoC 763486 c.117T>G synonymous_variant 0.25
rpoC 763492 c.123G>C synonymous_variant 0.23
rpoC 763504 c.135C>G synonymous_variant 0.2
rpoC 763507 c.138G>C synonymous_variant 0.19
rpoC 763511 p.Cys48Gly missense_variant 0.2
rpoC 763517 p.Lys50Gln missense_variant 0.19
rpoC 763528 c.159G>C synonymous_variant 0.17
rpoC 763531 c.162G>C synonymous_variant 0.19
rpoC 763532 p.Thr55Ser missense_variant 0.18
rpoC 763546 c.177A>G synonymous_variant 0.24
rpoC 763550 p.Tyr61Ala missense_variant 0.24
rpoC 763570 c.201G>C synonymous_variant 0.21
rpoC 763589 p.Ile74Val missense_variant 0.25
rpoC 763609 c.240C>G synonymous_variant 0.28
rpoC 763614 c.246_251delGACCCG disruptive_inframe_deletion 0.13
rpoC 763622 p.Ala85Thr missense_variant 0.13
rpoC 763627 c.258_259insAGCTCC conservative_inframe_insertion 0.17
rpoC 763630 c.261G>C synonymous_variant 0.18
rpoC 763633 c.264T>C synonymous_variant 0.18
rpoC 763642 c.273G>C synonymous_variant 0.36
rpoC 763660 c.291T>G synonymous_variant 0.29
rpoC 763666 c.297G>C synonymous_variant 0.27
rpoC 763669 c.300C>G synonymous_variant 0.27
rpoC 763675 c.306C>G synonymous_variant 0.25
rpoC 763696 c.327T>C synonymous_variant 0.14
rpoC 763699 c.330G>T synonymous_variant 0.14
rpoC 763708 c.339G>T synonymous_variant 0.14
rpoC 763711 c.342G>C synonymous_variant 0.14
rpoC 763715 p.Tyr116His missense_variant 0.11
rpoC 763723 c.354G>C synonymous_variant 0.11
rpoC 763727 p.Leu120Met missense_variant 0.12
rpoC 764365 c.996C>G synonymous_variant 0.29
rpoC 764470 c.1101C>G synonymous_variant 0.36
rpoC 764497 c.1128A>G synonymous_variant 0.33
rpoC 764498 p.Ser377Ala missense_variant 0.47
rpoC 764503 c.1134G>C synonymous_variant 0.31
rpoC 764521 c.1152T>C synonymous_variant 0.47
rpoC 764524 c.1155C>T synonymous_variant 0.32
rpoC 764527 c.1158C>T synonymous_variant 0.33
rpoC 764530 c.1161C>T synonymous_variant 0.33
rpoC 764533 c.1164C>T synonymous_variant 0.32
rpoC 764536 c.1167G>T synonymous_variant 0.43
rpoC 764537 p.Pro390Val missense_variant 0.25
rpoC 764540 p.Val391Ile missense_variant 0.21
rpoC 764545 c.1176C>G synonymous_variant 0.43
rpoC 764548 c.1179G>C synonymous_variant 0.6
rpoC 764549 p.Pro394Thr missense_variant 0.55
rpoC 764552 p.Gly395Asn missense_variant 0.2
rpoC 764557 p.Asn396Lys missense_variant 0.19
rpoC 764561 p.Pro398Ala missense_variant 0.44
rpoC 764566 c.1197C>G synonymous_variant 0.62
rpoC 764575 c.1206T>G synonymous_variant 0.54
rpoC 764576 p.Ser403Ala missense_variant 0.19
rpoC 764581 c.1212T>C synonymous_variant 0.62
rpoC 764582 p.Leu405Met missense_variant 0.62
rpoC 764605 c.1236G>C synonymous_variant 0.69
rpoC 764611 c.1242G>C synonymous_variant 0.69
rpoC 764620 c.1251G>C synonymous_variant 0.38
rpoC 764621 c.1252_1254delCTCinsTTG synonymous_variant 0.38
rpoC 764632 c.1263T>C synonymous_variant 0.67
rpoC 764635 c.1266C>G synonymous_variant 0.29
rpoC 764641 c.1272C>T synonymous_variant 0.32
rpoC 764650 c.1281G>T synonymous_variant 0.53
rpoC 764660 p.Val431Ile missense_variant 0.19
rpoC 764665 c.1296C>G synonymous_variant 0.2
rpoC 764671 c.1302G>C synonymous_variant 0.27
rpoC 764672 p.Gln435Glu missense_variant 0.21
rpoC 764677 c.1308C>G synonymous_variant 0.2
rpoC 764683 c.1314G>C synonymous_variant 0.21
rpoC 764686 c.1317C>T synonymous_variant 0.23
rpoC 764689 c.1320G>A synonymous_variant 0.21
rpoC 764695 c.1326T>C synonymous_variant 0.23
rpoC 764701 c.1332C>G synonymous_variant 0.23
rpoC 764705 p.Leu446Lys missense_variant 0.25
rpoC 764713 c.1344G>T synonymous_variant 0.17
rpoC 764716 c.1347G>C synonymous_variant 0.42
rpoC 764719 c.1350G>A synonymous_variant 0.2
rpoC 766647 p.Asp1093Val missense_variant 0.25
rpoC 767179 c.3810C>T synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781796 p.Met79Ile missense_variant 0.12
rpsL 781817 c.258G>T synonymous_variant 0.17
rpsL 781829 c.270G>T synonymous_variant 0.12
rpsL 781832 c.273T>C synonymous_variant 0.13
rpsL 781838 c.279G>C synonymous_variant 0.14
fbiC 1305004 p.Glu692Gln missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.5
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.5
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.5
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.5
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.5
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.5
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.29
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.25
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.4
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.36
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.31
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.2
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.17
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.15
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.25
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.17
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.18
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.25
rrs 1472496 n.651T>G non_coding_transcript_exon_variant 0.27
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.27
rrs 1472507 n.662C>T non_coding_transcript_exon_variant 0.25
rrs 1472513 n.668T>C non_coding_transcript_exon_variant 0.23
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.12
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.12
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.32
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.26
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.26
rrs 1472571 n.726G>A non_coding_transcript_exon_variant 0.25
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.33
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.17
rrs 1472606 n.761C>G non_coding_transcript_exon_variant 0.26
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.56
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.26
rrs 1472645 n.800G>C non_coding_transcript_exon_variant 0.2
rrs 1472655 n.810G>T non_coding_transcript_exon_variant 0.38
rrs 1472660 n.815T>A non_coding_transcript_exon_variant 0.25
rrs 1472666 n.821G>T non_coding_transcript_exon_variant 0.22
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.29
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.43
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.43
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.5
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.33
rrs 1472803 n.958T>C non_coding_transcript_exon_variant 0.29
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.33
rrs 1472887 n.1042G>C non_coding_transcript_exon_variant 0.25
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.17
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.2
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.3
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.25
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.3
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.17
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.17
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.18
rrs 1473097 n.1252G>A non_coding_transcript_exon_variant 0.2
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.21
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.27
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.2
rrs 1473109 n.1264T>G non_coding_transcript_exon_variant 0.12
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.19
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.31
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.29
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.19
rrs 1473134 n.1289T>C non_coding_transcript_exon_variant 0.26
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.42
rrs 1473147 n.1302G>A non_coding_transcript_exon_variant 0.26
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.21
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.42
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.35
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.12
rrs 1473269 n.1424C>T non_coding_transcript_exon_variant 0.33
rrs 1473270 n.1425G>A non_coding_transcript_exon_variant 0.13
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.47
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.31
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.4
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.29
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.4
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.14
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.15
rrs 1473349 n.1504G>A non_coding_transcript_exon_variant 0.18
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.18
rrl 1474383 n.726G>T non_coding_transcript_exon_variant 0.2
rrl 1474476 n.819C>T non_coding_transcript_exon_variant 1.0
rrl 1474488 n.831G>C non_coding_transcript_exon_variant 1.0
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 1.0
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 1.0
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 1.0
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 1.0
rrl 1474516 n.859C>G non_coding_transcript_exon_variant 1.0
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 1.0
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.75
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.4
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 0.33
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.33
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.33
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.33
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.4
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.33
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.36
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.18
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.22
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.4
rrl 1475752 n.2095C>G non_coding_transcript_exon_variant 0.5
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.5
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.5
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.5
rrl 1475776 n.2119G>C non_coding_transcript_exon_variant 0.5
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.29
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.22
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.56
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.38
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.38
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.33
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.33
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.43
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.5
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.4
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.25
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.38
rrl 1476195 n.2538C>T non_coding_transcript_exon_variant 0.25
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.43
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.43
rrl 1476211 n.2554G>A non_coding_transcript_exon_variant 0.45
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.55
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.18
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.55
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.62
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.62
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.67
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.67
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.8
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.67
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.78
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.78
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.78
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.78
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.78
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.78
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.67
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.4
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.33
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.45
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.48
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.55
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.75
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.83
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.58
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.56
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.62
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.56
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.71
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.11
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.52
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.48
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.42
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.61
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.38
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.38
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.33
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.24
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.14
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.15
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.13
fabG1 1673553 p.Asp38Glu missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102817 p.Leu76Val missense_variant 0.17
katG 2155389 c.723C>G synonymous_variant 1.0
PPE35 2170062 p.Ala184Gly missense_variant 0.67
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 1.0
Rv1979c 2223166 c.-2C>T upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.33
Rv2752c 3066244 c.-53G>C upstream_gene_variant 0.14
thyX 3067474 p.Pro158Ala missense_variant 1.0
ald 3087224 p.Glu135Asp missense_variant 0.17
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474054 p.Phe16Leu missense_variant 0.25
fprA 3474057 p.Phe17Leu missense_variant 0.4
fprA 3474967 p.Ser321Ala missense_variant 0.2
Rv3236c 3612571 c.546C>T synonymous_variant 1.0
Rv3236c 3612928 c.189C>T synonymous_variant 0.22
alr 3840843 p.Leu193Pro missense_variant 0.11
clpC1 4040069 c.636G>C synonymous_variant 0.16
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244355 p.Phe375Ile missense_variant 0.2
embB 4247016 p.Ser168Trp missense_variant 0.3
embB 4248328 c.1815G>C synonymous_variant 0.25
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338205 p.Val106Gly missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0