TB-Profiler result

Run: SRR6832189
Summary

Run ID: SRR6832189

Sample name:

Date: 04-04-2023 17:16:49

Number of reads: 431266

Percentage reads mapped: 99.71

Strain: lineage4.3.3

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
lineage4.3.3 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247469 p.Tyr319Ser 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761311 p.Pro502Leu missense_variant 0.12
rpoC 764667 p.Gly433Ala missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302831 c.-100C>A upstream_gene_variant 0.14
fbiC 1303095 c.165G>A synonymous_variant 1.0
fbiC 1303819 p.Ala297Ser missense_variant 0.22
fbiC 1304962 p.Trp678Gly missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101913 c.1129delT frameshift_variant 0.2
katG 2156196 c.-85C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289806 c.-565A>T upstream_gene_variant 0.4
pncA 2289832 c.-592delT upstream_gene_variant 0.33
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746249 c.1350C>T synonymous_variant 0.2
folC 2746340 p.Ala420Val missense_variant 1.0
folC 2747288 p.Pro104Gln missense_variant 0.2
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
thyX 3068038 c.-93C>T upstream_gene_variant 0.17
thyX 3068151 c.-206T>C upstream_gene_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473946 c.-61T>C upstream_gene_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641446 p.Thr302Ser missense_variant 0.14
fbiB 3642520 p.Asp329Val missense_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242693 p.Arg944Leu missense_variant 0.18
ubiA 4269864 c.-31C>T upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0