TB-Profiler result

Run: SRR998689
Summary

Run ID: SRR998689

Sample name:

Date: 04-04-2023 23:31:58

Number of reads: 2520807

Percentage reads mapped: 93.21

Strain: lineage4.1.3

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 1.0
lineage4.1.3 Euro-American T;X;H None 0.06
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
katG 2155168 p.Ser315Thr missense_variant 0.12 isoniazid
pncA 2288853 p.Val130Ala missense_variant 0.15 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.16 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
gyrB 6507 p.Ala423Val missense_variant 0.89
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9656 c.2355C>G synonymous_variant 0.95
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765187 c.1818C>T synonymous_variant 0.92
rpoC 766012 c.2643C>G synonymous_variant 0.92
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775973 p.Leu836Phe missense_variant 0.89
mmpL5 776411 c.2070T>C synonymous_variant 0.89
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673468 p.Lys10Thr missense_variant 0.94
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154116 p.Ile666Val missense_variant 0.82
katG 2156007 c.105C>T synonymous_variant 0.96
PPE35 2170748 c.-136C>T upstream_gene_variant 0.95
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067339 p.His203Asn missense_variant 0.13
thyA 3073806 c.666C>G synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878588 c.-81G>A upstream_gene_variant 0.85
clpC1 4038857 c.1848C>A synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4248758 c.2245C>T synonymous_variant 0.92
whiB6 4338595 c.-75delG upstream_gene_variant 1.0