TB-Profiler result

Run: SRR7535045
Summary

Run ID: SRR7535045

Sample name:

Date: 04-04-2023 19:42:16

Number of reads: 1971647

Percentage reads mapped: 99.63

Strain: lineage4.3.4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.95
lineage4.3.4 Euro-American (LAM) LAM RD174 0.96
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.98
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.98
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 761155 p.Ser450Leu missense_variant 0.93 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2289054 p.Asp63Gly missense_variant 0.98 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.96 ethambutol
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
ethA 4327033 p.Tyr147* stop_gained 0.5 ethionamide
ethA 4326694 c.440_779del frameshift_variant 1.0 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
gyrB 6140 p.Val301Leu missense_variant 0.94
gyrA 7362 p.Glu21Gln missense_variant 0.96
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.94
rpoC 767083 c.3714C>T synonymous_variant 0.96
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.95
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.9
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.31
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
alr 3840719 c.702A>G synonymous_variant 0.96
alr 3840869 c.552C>G synonymous_variant 0.96
rpoA 3877964 p.Arg182Trp missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242425 p.Arg855Gly missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269311 p.Trp175Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.88