TB-Profiler result

Run: SRR998847
Summary

Run ID: SRR998847

Sample name:

Date: 04-04-2023 23:38:49

Number of reads: 2520622

Percentage reads mapped: 99.25

Strain: lineage4.1.3

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 0.96
lineage4.1 Euro-American T;X;H None 0.91
lineage4.1.3 Euro-American T;X;H None 0.91
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 761111 p.Asp435Glu missense_variant 0.85 rifampicin
rpoB 761128 p.Ser441Leu missense_variant 0.86 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 0.95 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.93 isoniazid
pncA 2288826 p.Val139Ala missense_variant 0.93 pyrazinamide
gid 4407967 p.Leu79Ser missense_variant 0.8 streptomycin
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
gyrB 6446 p.Ala403Ser missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9557 c.2256G>C synonymous_variant 0.91
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 1.0
fbiC 1304610 c.1680C>T synonymous_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674434 p.Val78Ala missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.15
katG 2155503 c.609C>T synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474428 p.Val141Ala missense_variant 0.14
fprA 3475159 p.Asn385Asp missense_variant 0.12
embC 4240671 p.Thr270Ile missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
aftB 4269351 c.-515C>T upstream_gene_variant 0.15
ubiA 4269387 p.Glu149Asp missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0