TB-Profiler result

Run: SRR3647353
Summary

Run ID: SRR3647353

Sample name:

Date: 04-04-2023 05:21:26

Number of reads: 7925458

Percentage reads mapped: 98.23

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 0.97
lineage4.2 Euro-American H;T;LAM None 0.87
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.88
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.His445Leu missense_variant 0.87 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.87 isoniazid
gid 4407695 p.Glu170* stop_gained 0.87 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 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.99
mshA 576077 c.730C>T synonymous_variant 0.9
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.97
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.87
ald 3086742 c.-78A>C upstream_gene_variant 0.9
ald 3086788 c.-32T>C upstream_gene_variant 0.94
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612469 c.648A>G synonymous_variant 0.85
alr 3841567 c.-147A>G upstream_gene_variant 0.91
rpoA 3878613 c.-113_-107delCAACCCA upstream_gene_variant 0.61
rpoA 3878630 c.-124delC upstream_gene_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.11