TB-Profiler result

Run: ERR6865980
Summary

Run ID: ERR6865980

Sample name:

Date: 02-04-2023 03:11:23

Number of reads: 2170587

Percentage reads mapped: 99.75

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 0.71
lineage4.3.4 Euro-American (LAM) LAM RD174 0.72
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.73
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 0.68 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.7 isoniazid
pncA 2288895 p.Leu116Pro missense_variant 0.62 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.82 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 0.67
rpoB 761889 p.Val695Leu missense_variant 0.3
rpoC 764995 c.1626C>G synonymous_variant 0.83
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777185 c.1296G>A synonymous_variant 0.31
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801009 c.201A>G synonymous_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473645 n.-12delT upstream_gene_variant 0.62
rrl 1474296 n.639T>G non_coding_transcript_exon_variant 0.5
rrl 1474645 n.988G>T non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747453 p.Arg49Gln missense_variant 0.74
Rv2752c 3065517 c.675C>T synonymous_variant 0.43
thyA 3073868 p.Thr202Ala missense_variant 0.79
thyA 3074361 c.111T>C synonymous_variant 0.72
ald 3086788 c.-32T>C upstream_gene_variant 0.8
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.7
fprA 3474299 p.Asp98Gly missense_variant 0.29
Rv3236c 3612009 p.Ala370Thr missense_variant 0.71
clpC1 4038287 c.2418C>T synonymous_variant 0.79
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244471 c.1239C>T synonymous_variant 0.26
embB 4248736 c.2223G>T synonymous_variant 0.65
ethA 4328317 c.-844C>T upstream_gene_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338600 c.-79T>C upstream_gene_variant 0.73
gid 4408054 p.Leu50Arg missense_variant 0.71
gid 4408156 p.Leu16Arg missense_variant 0.75