TB-Profiler result

Run: ERR4553807

Summary

Run ID: ERR4553807

Sample name:

Date: 01-04-2023 06:21:35

Number of reads: 2224582

Percentage reads mapped: 99.78

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
lineage4.3.4 Euro-American (LAM) LAM RD174 0.94
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.97
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
embB 4247429 p.Met306Val missense_variant 0.4 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 0.99
gyrA 9304 p.Gly668Asp missense_variant 0.92
mshA 576108 p.Ala254Gly missense_variant 0.27
rpoC 764995 c.1626C>G synonymous_variant 0.82
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102295 p.Thr250Ala missense_variant 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747169 p.Lys144Glu missense_variant 0.95
Rv2752c 3065293 p.Val300Ala missense_variant 0.98
thyA 3074158 p.Ser105Phe missense_variant 0.93
thyA 3074495 c.-24C>T upstream_gene_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 0.98
fbiD 3339734 p.Ala206Gly missense_variant 0.27
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.93
Rv3236c 3612009 p.Ala370Thr missense_variant 0.85
clpC1 4038287 c.2418C>T synonymous_variant 0.92
embC 4239763 c.-100C>T upstream_gene_variant 0.99
embA 4242526 c.-707C>G upstream_gene_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408051 p.Asn51Thr missense_variant 0.96
gid 4408156 p.Leu16Arg missense_variant 0.75