TB-Profiler result

Run: SRR12830370

Summary

Run ID: SRR12830370

Sample name:

Date: 03-04-2023 06:58:25

Number of reads: 407169

Percentage reads mapped: 99.84

Strain: lineage4.3.4;lineage4.3.3

Drug-resistance: Sensitive


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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 0.32
lineage4.3.4 Euro-American (LAM) LAM RD174 0.61
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
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 6084 p.Gly282Asp missense_variant 0.2
gyrA 7003 c.-299C>T upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7596 p.Met99Val missense_variant 0.12
gyrA 8040 p.Gly247Ser missense_variant 0.46
gyrA 8390 c.1089C>A synonymous_variant 0.14
gyrA 9207 p.Lys636Glu missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9570 p.Arg757Ser missense_variant 0.2
ccsA 620229 p.Phe113Leu missense_variant 0.15
rpoB 760080 p.Asp92Tyr missense_variant 0.2
rpoB 761693 c.1887G>T synonymous_variant 0.13
rpoB 762805 p.Gly1000Val missense_variant 0.18
rpoB 762882 p.Lys1026Glu missense_variant 0.17
rpoC 763574 p.Arg69Cys missense_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777033 p.Ala483Asp missense_variant 0.15
mmpL5 778265 p.Met72Ile missense_variant 0.2
mmpL5 778462 p.Ala7Ser missense_variant 0.12
mmpL5 778478 c.3G>A start_lost 0.13
mmpR5 779221 p.Gly78Trp missense_variant 0.17
mmpS5 779481 c.-576G>A upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800997 c.189C>T synonymous_variant 0.14
fbiC 1303076 p.Thr49Asn missense_variant 0.18
fbiC 1304337 c.1407C>T synonymous_variant 0.56
Rv1258c 1406140 p.Arg401Cys missense_variant 0.2
Rv1258c 1406306 c.1035C>T synonymous_variant 0.12
Rv1258c 1406740 p.His201Asn missense_variant 0.15
Rv1258c 1406800 p.Phe181Ile missense_variant 0.13
Rv1258c 1406855 c.486C>A synonymous_variant 0.17
Rv1258c 1406981 c.360C>T synonymous_variant 0.29
Rv1258c 1407230 c.111C>A synonymous_variant 0.2
Rv1258c 1407403 c.-63G>T upstream_gene_variant 0.15
embR 1416277 c.1071C>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473101 n.1256C>T non_coding_transcript_exon_variant 0.25
rrl 1473401 n.-257G>T upstream_gene_variant 0.18
rrl 1474110 n.453A>C non_coding_transcript_exon_variant 0.5
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 0.29
rrl 1475649 n.1992A>G non_coding_transcript_exon_variant 0.5
rpsA 1833435 c.-107G>A upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102308 c.735G>A synonymous_variant 0.47
katG 2156140 c.-29C>T upstream_gene_variant 0.13
PPE35 2170515 p.Gly33Glu missense_variant 0.18
Rv1979c 2222000 p.Val389Leu missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223324 c.-160G>A upstream_gene_variant 0.29
pncA 2289195 p.Gly16Val missense_variant 0.14
pncA 2289873 c.-632C>A upstream_gene_variant 0.25
kasA 2518056 c.-59G>T upstream_gene_variant 0.22
kasA 2518506 p.Ala131Val missense_variant 0.12
kasA 2518919 p.Gly269Ser missense_variant 0.37
kasA 2519094 p.Arg327His missense_variant 0.14
ahpC 2726297 c.105C>T synonymous_variant 0.15
folC 2747423 p.Ser59* stop_gained 0.13
pepQ 2860010 p.Ala137Thr missense_variant 0.2
Rv2752c 3065293 p.Val300Ala missense_variant 0.73
Rv2752c 3065465 p.Asp243His missense_variant 0.13
Rv2752c 3065524 p.His223Leu missense_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087116 c.297G>T synonymous_variant 0.14
ald 3087538 p.Leu240Arg missense_variant 0.12
fbiD 3339291 c.174G>C synonymous_variant 0.12
Rv3083 3449854 p.Met451Val missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568646 c.33delC frameshift_variant 0.14
Rv3236c 3612009 p.Ala370Thr missense_variant 0.62
fbiB 3642050 c.516G>T synonymous_variant 0.12
fbiB 3642352 p.Gly273Val missense_variant 0.14
rpoA 3877613 p.Ile299Val missense_variant 0.12
rpoA 3877999 p.Pro170Leu missense_variant 0.14
rpoA 3878466 c.42C>A synonymous_variant 0.15
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038326 p.Glu793Asp missense_variant 0.17
clpC1 4038344 p.Glu787Asp missense_variant 0.17
clpC1 4040288 c.417C>A synonymous_variant 0.13
embC 4239763 c.-100C>T upstream_gene_variant 0.9
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243306 p.Leu25Arg missense_variant 0.13
embA 4245092 c.1860C>T synonymous_variant 0.13
embA 4245170 c.1938G>A synonymous_variant 0.13
embA 4245268 p.Asn679Ile missense_variant 0.13
embB 4247884 c.1371C>A synonymous_variant 0.65
embB 4248988 c.2475C>A synonymous_variant 0.14
aftB 4267898 c.939T>C synonymous_variant 0.11
aftB 4268772 p.Trp22* stop_gained 0.18
aftB 4269330 c.-494C>T upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338649 c.-128C>A upstream_gene_variant 0.13
gid 4408156 p.Leu16Arg missense_variant 1.0