TB-Profiler result

Run: SRR15316264
Summary

Run ID: SRR15316264

Sample name:

Date: 03-04-2023 13:20:28

Number of reads: 8864080

Percentage reads mapped: 99.54

Strain: lineage4.5

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
lineage4.5 Euro-American H;T RD122 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 0.98 ethambutol
gid 4408154 c.48delT frameshift_variant 1.0 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 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoB 761360 c.1554T>C synonymous_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776495 c.1986G>C synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154124 p.Asp663Ala missense_variant 1.0
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2222057 p.Asp370Asn missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519122 c.1008G>C synonymous_variant 1.0
eis 2714984 p.Ala117Thr missense_variant 1.0
thyX 3067481 c.465C>G synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640407 c.-136G>T upstream_gene_variant 1.0
fbiA 3640823 p.Arg94His missense_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268596 p.Tyr81His missense_variant 1.0
aftB 4268719 p.Asn40Asp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408152 c.-73_50del frameshift_variant&start_lost 1.0