TB-Profiler result

Run: SRR15316421
Summary

Run ID: SRR15316421

Sample name:

Date: 03-04-2023 13:30:34

Number of reads: 8841605

Percentage reads mapped: 99.5

Strain: lineage4.2.2

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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
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 761140 p.His445Arg missense_variant 1.0 rifampicin
rpoB 761149 p.Arg448Gln missense_variant 1.0 rifampicin
katG 2155729 p.Arg128Pro missense_variant 1.0 isoniazid
pncA 2288826 p.Val139Ala missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
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
rpsA 1833747 p.Ser69Phe missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518496 c.382C>T synonymous_variant 0.99
ahpC 2726146 c.-47_-46insT upstream_gene_variant 0.99
folC 2746849 c.750G>A synonymous_variant 0.99
ribD 2987166 p.Gly110Ser missense_variant 1.0
Rv2752c 3066276 c.-85G>A upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C 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
Rv3236c 3612469 c.648A>G synonymous_variant 0.99
Rv3236c 3612752 p.Ala122Val missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326135 p.Pro447Thr missense_variant 1.0
ethA 4326363 p.Gly371Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408048 p.Cys52Phe missense_variant 0.95