TB-Profiler result

Run: ERR1034741
Summary

Run ID: ERR1034741

Sample name:

Date: 31-03-2023 09:36:49

Number of reads: 21976750

Percentage reads mapped: 99.58

Strain: lineage4.1.1.3

Drug-resistance: HR-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
lineage4.1 Euro-American T;X;H None 0.64
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.66
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.65
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
fabG1 1673423 c.-17G>T upstream_gene_variant 0.36 isoniazid, ethionamide
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 761889 p.Val695Leu missense_variant 0.38
rpoC 765150 p.Gly594Glu missense_variant 0.64
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778509 p.Ala133Thr missense_variant 0.65
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801009 c.201A>G synonymous_variant 0.32
fbiC 1302954 c.24G>A synonymous_variant 0.65
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674952 p.Pro251Ala missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154678 c.1434G>C synonymous_variant 0.62
PPE35 2169320 p.Leu431Phe missense_variant 0.27
PPE35 2169405 p.Asn403Ser missense_variant 0.68
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.34
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726409 p.Asp73His missense_variant 0.63
Rv2752c 3065517 c.675C>T synonymous_variant 0.35
thyA 3073806 c.666C>G synonymous_variant 0.3
ald 3086788 c.-32T>C upstream_gene_variant 0.66
Rv3083 3448439 c.-64delA upstream_gene_variant 0.35
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.61
fprA 3474299 p.Asp98Gly missense_variant 0.34
rpoA 3878595 c.-88C>T upstream_gene_variant 0.12
clpC1 4038857 c.1848C>A synonymous_variant 0.13
embC 4242425 p.Arg855Gly missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.66
embC 4242822 p.Val987Gly missense_variant 0.27
embB 4249408 c.2895G>A synonymous_variant 0.66
embB 4249678 c.3165C>A synonymous_variant 0.7
ethA 4328317 c.-844C>T upstream_gene_variant 0.37
whiB6 4338595 c.-75delG upstream_gene_variant 1.0