TB-Profiler result

Run: SRR2100067
Summary

Run ID: SRR2100067

Sample name:

Date: 03-04-2023 22:44:15

Number of reads: 8178303

Percentage reads mapped: 75.66

Strain: lineage4.3.3

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 0.14 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759831 p.Thr9Pro missense_variant 0.34
rpoB 762249 p.Leu815Val missense_variant 0.22
rpoC 762836 c.-534C>G upstream_gene_variant 0.3
rpoC 762896 c.-474G>C upstream_gene_variant 0.14
rpoC 762929 c.-441G>C upstream_gene_variant 0.18
rpoC 762932 c.-438G>C upstream_gene_variant 0.16
rpoC 762947 c.-423C>G upstream_gene_variant 0.12
rpoC 763115 c.-255T>C upstream_gene_variant 0.1
rpoC 763666 c.297G>C synonymous_variant 0.11
rpoC 763696 c.327T>C synonymous_variant 0.14
rpoC 764371 c.1002G>C synonymous_variant 0.11
rpoC 764551 c.1182G>C synonymous_variant 0.14
rpoC 764561 p.Pro398Ala missense_variant 0.19
rpoC 764566 c.1197C>G synonymous_variant 0.22
rpoC 764575 c.1206T>G synonymous_variant 0.19
rpoC 764581 c.1212T>C synonymous_variant 0.19
rpoC 764582 p.Leu405Met missense_variant 0.18
rpoC 764611 c.1242G>C synonymous_variant 0.23
rpoC 764632 c.1263T>C synonymous_variant 0.15
rpoC 764635 c.1266C>G synonymous_variant 0.14
rpoC 764650 c.1281G>T synonymous_variant 0.14
rpoC 764662 c.1293G>C synonymous_variant 0.1
rpoC 764677 c.1308C>G synonymous_variant 0.15
rpoC 764683 c.1314G>C synonymous_variant 0.14
rpoC 764692 c.1323C>T synonymous_variant 0.12
rpoC 764705 p.Leu446Ala missense_variant 0.13
rpoC 764716 c.1347G>C synonymous_variant 0.1
rpoC 764995 c.1626C>G synonymous_variant 0.94
rpoC 767305 p.Tyr1312* stop_gained 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461019 c.-26C>A upstream_gene_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.13
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.14
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.14
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.13
rrs 1472382 n.537G>A non_coding_transcript_exon_variant 0.16
rrs 1472389 n.544G>A non_coding_transcript_exon_variant 0.16
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.14
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.23
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.24
rrs 1472571 n.726G>A non_coding_transcript_exon_variant 0.23
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.25
rrs 1472606 n.761C>G non_coding_transcript_exon_variant 0.23
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.19
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.18
rrs 1472645 n.800G>C non_coding_transcript_exon_variant 0.11
rrs 1472714 n.869A>T non_coding_transcript_exon_variant 0.18
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.26
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.17
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.19
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.18
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.19
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.19
rrs 1472982 n.1137G>A non_coding_transcript_exon_variant 0.21
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.18
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.18
rrs 1472993 n.1148G>T non_coding_transcript_exon_variant 0.18
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.2
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.15
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.15
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.16
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.11
rrs 1473134 n.1289T>C non_coding_transcript_exon_variant 0.15
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.12
rrs 1473147 n.1302G>A non_coding_transcript_exon_variant 0.12
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.17
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.17
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.12
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.24
rrl 1474488 n.831G>C non_coding_transcript_exon_variant 0.11
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.12
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.12
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.12
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.12
rrl 1474516 n.859C>G non_coding_transcript_exon_variant 0.16
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.19
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.21
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.2
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 0.19
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.15
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.14
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.14
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.14
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.14
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.1
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.1
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.17
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.17
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.16
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.18
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.18
rrl 1475672 n.2015C>T non_coding_transcript_exon_variant 0.1
rrl 1475692 n.2035G>C non_coding_transcript_exon_variant 0.17
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.2
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.2
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.21
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.18
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.18
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.18
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.19
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.26
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.29
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.24
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.21
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.18
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.13
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.97
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.17
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.29
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.28
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.27
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.27
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.32
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.27
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.23
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.23
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.24
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.17
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.1
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.11
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.17
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.18
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.18
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.35
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.31
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.18
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.14
rpsA 1834427 p.Ile296Val missense_variant 0.14
rpsA 1834431 p.Val297Ala missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.17
PPE35 2169866 c.747G>C synonymous_variant 0.26
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.99
eis 2714366 p.Val323Leu missense_variant 0.25
eis 2715586 c.-254G>C upstream_gene_variant 0.4
pepQ 2859381 c.1038C>G synonymous_variant 0.21
ribD 2986872 p.Thr12Ala missense_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.16
Rv2752c 3064552 p.Arg547Pro missense_variant 0.3
Rv2752c 3064741 p.Gly484Ala missense_variant 0.25
Rv2752c 3065824 p.Pro123Leu missense_variant 0.99
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3641955 p.Gly141Arg missense_variant 0.22
fbiB 3642734 c.1200G>C synonymous_variant 0.15
rpoA 3878238 p.Asp90Glu missense_variant 0.16
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.24
clpC1 4039932 p.Gly258Val missense_variant 0.3
embC 4242425 p.Arg855Gly missense_variant 0.21
embC 4242476 p.Pro872Ala missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.31
ubiA 4269529 p.Ala102Gly missense_variant 0.24
ethA 4327672 c.-199G>A upstream_gene_variant 0.33
whiB6 4338522 c.-2_-1insGTT upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0