TB-Profiler result

Run: ERR4024759
Summary

Run ID: ERR4024759

Sample name:

Date: 01-04-2023 04:08:07

Number of reads: 2328285

Percentage reads mapped: 99.71

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 0.21
lineage4.3.4 Euro-American (LAM) LAM RD174 0.27
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.25
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 0.32 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.24 isoniazid
pncA 2288895 p.Leu116Pro missense_variant 0.25 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.33 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 761455 p.Glu550Gly missense_variant 0.29
rpoB 761889 p.Val695Leu missense_variant 0.77
rpoC 764995 c.1626C>G synonymous_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777185 c.1296G>A synonymous_variant 0.78
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801009 c.201A>G synonymous_variant 0.75
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473645 n.-12delT upstream_gene_variant 0.38
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.75
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747453 p.Arg49Gln missense_variant 0.12
Rv2752c 3065517 c.675C>T synonymous_variant 0.72
thyA 3073868 p.Thr202Ala missense_variant 0.19
thyA 3074361 c.111T>C synonymous_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.16
fprA 3474299 p.Asp98Gly missense_variant 0.75
Rv3236c 3612009 p.Ala370Thr missense_variant 0.31
rpoA 3878580 c.-74_-73insCAACCCA upstream_gene_variant 0.26
rpoA 3878595 c.-88C>T upstream_gene_variant 0.29
rpoA 3878635 c.-128C>T upstream_gene_variant 0.2
clpC1 4038287 c.2418C>T synonymous_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244471 c.1239C>T synonymous_variant 0.75
embB 4248736 c.2223G>T synonymous_variant 0.22
ethA 4328317 c.-844C>T upstream_gene_variant 0.79
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338600 c.-79T>C upstream_gene_variant 0.21
gid 4408054 p.Leu50Arg missense_variant 0.28
gid 4408156 p.Leu16Arg missense_variant 0.28