TB-Profiler result

Run: SRR18715189
Summary

Run ID: SRR18715189

Sample name:

Date: 03-04-2023 20:23:06

Number of reads: 2645920

Percentage reads mapped: 99.78

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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247730 p.Gly406Ala 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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9647 c.2346C>G synonymous_variant 0.22
mshA 576113 p.Arg256Gly missense_variant 0.65
mshA 576456 p.Val370Gly missense_variant 0.25
mshA 576613 c.1266A>C synonymous_variant 0.44
mshA 576616 c.1269G>C synonymous_variant 0.43
rpoB 762423 p.Ile873Phe missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.34
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.98
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 2102817 p.Leu76Val missense_variant 0.15
katG 2156196 c.-85C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.21
folC 2746340 p.Ala420Val missense_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.31
Rv2752c 3064823 p.Val457Leu missense_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.33
whiB7 3568428 c.252A>G synonymous_variant 0.5
whiB7 3568431 c.249C>G synonymous_variant 0.43
rpoA 3878597 c.-90G>C upstream_gene_variant 0.5
rpoA 3878637 c.-130G>C upstream_gene_variant 0.67
rpoA 3878641 c.-134C>G upstream_gene_variant 0.92
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246527 p.Ala5Gly missense_variant 0.26
embB 4247016 p.Ser168Trp missense_variant 0.2
embB 4247033 p.Ser174Arg missense_variant 0.17
embB 4248328 c.1815G>C synonymous_variant 0.24
whiB6 4338200 p.Asp108His missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408010 p.Val65Phe missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0