TB-Profiler result

Run: SRR6511642
Summary

Run ID: SRR6511642

Sample name:

Date: 04-04-2023 15:16:12

Number of reads: 1032504

Percentage reads mapped: 99.74

Strain: lineage4.3.4.2

Drug-resistance: MDR-TB

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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
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
pncA 2288749 p.Ala165Thr missense_variant 0.11 pyrazinamide
pncA 2289199 p.Glu15* stop_gained 1.0 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
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 6817 c.-485G>A upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9139 p.Gln613Arg missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9335 c.2034G>A synonymous_variant 0.11
gyrA 9347 c.2046G>A synonymous_variant 0.1
mshA 576201 p.Arg285His missense_variant 0.15
mshA 576590 p.Arg415Trp missense_variant 0.13
rpoB 759776 c.-31T>G upstream_gene_variant 0.14
rpoB 760963 p.Gly386Asp missense_variant 0.11
rpoB 761270 c.1464C>T synonymous_variant 0.11
rpoC 763814 c.447delC frameshift_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 779362 c.-882G>A upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304579 p.Arg550His missense_variant 0.1
Rv1258c 1406922 p.Asp140Gly missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474874 n.1217A>G non_coding_transcript_exon_variant 0.15
inhA 1674415 p.Ala72Thr missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155034 p.Gly360Ser missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289100 p.Lys48* stop_gained 0.11
pncA 2289238 p.Arg2Trp missense_variant 0.13
pncA 2289441 c.-200C>T upstream_gene_variant 0.12
eis 2715109 p.Val75Ala missense_variant 0.12
eis 2715361 c.-29G>A upstream_gene_variant 0.13
eis 2715430 c.-98C>T upstream_gene_variant 0.11
folC 2746637 p.Leu321Pro missense_variant 0.17
folC 2747459 p.Leu47Pro missense_variant 0.1
folC 2747610 c.-12G>A upstream_gene_variant 0.11
folC 2747656 c.-58G>A upstream_gene_variant 0.12
pepQ 2860214 p.Pro69Ala missense_variant 0.11
ribD 2986829 c.-10A>G upstream_gene_variant 0.1
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474501 c.495T>A synonymous_variant 0.12
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiA 3640395 c.-148T>C upstream_gene_variant 0.11
rpoA 3878043 c.465G>A synonymous_variant 0.13
rpoA 3878048 p.Ala154Thr missense_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239716 c.-147G>T upstream_gene_variant 0.11
embC 4239763 c.-100C>T upstream_gene_variant 1.0
embC 4240329 p.Thr156Ile missense_variant 0.12
embC 4241687 p.Thr609Ala missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243198 c.-34delC upstream_gene_variant 1.0
embB 4247031 p.Arg173His missense_variant 0.12
ubiA 4269719 p.Ala39Thr missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0