TB-Profiler result

Run: SRR998774

Summary

Run ID: SRR998774

Sample name:

Date: 04-04-2023 23:35:31

Number of reads: 1568938

Percentage reads mapped: 99.22

Strain: lineage4.1.3

Drug-resistance: Pre-XDR-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 0.93
lineage4.1.3 Euro-American T;X;H None 0.96
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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.86 isoniazid
pncA 2289222 p.Val7Gly missense_variant 0.91 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.96 ethambutol
ethA 4326270 c.1203delT frameshift_variant 0.98 ethionamide
gid 4407967 p.Leu79Ser missense_variant 0.94 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
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 9557 c.2256G>C synonymous_variant 0.84
rpoC 765150 p.Gly594Glu missense_variant 0.94
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777507 p.Ser325Thr missense_variant 0.12
mmpR5 779252 p.Asp88Gly missense_variant 0.89
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 1.0
fbiC 1302999 c.69C>T synonymous_variant 0.13
fbiC 1304610 c.1680C>T synonymous_variant 0.95
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.94
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.94
embC 4242972 p.Glu1037Gly missense_variant 0.1
embA 4243217 c.-16C>A upstream_gene_variant 1.0
embA 4244323 p.Ala364Val missense_variant 0.14
embA 4244877 p.Ala549Thr missense_variant 0.12
ethA 4326532 c.942C>T synonymous_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338661 c.-140C>T upstream_gene_variant 0.98