TB-Profiler result

Run: SRR21576729
Summary

Run ID: SRR21576729

Sample name:

Date: 04-04-2023 02:16:33

Number of reads: 1880599

Percentage reads mapped: 97.32

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 0.99
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 761095 p.Leu430Pro missense_variant 1.0 rifampicin
rpoB 761139 p.His445Tyr missense_variant 0.99 rifampicin
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.1 streptomycin
inhA 1674481 p.Ser94Ala missense_variant 0.98 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288779 p.Val155Met missense_variant 0.97 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
gid 4407851 c.351delG frameshift_variant 0.97 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 0.98
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620029 c.139C>T synonymous_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779228 p.Ile80Ser missense_variant 0.97
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.45
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rrs 1472767 n.924_925delCC non_coding_transcript_exon_variant 0.11
rrl 1475151 n.1494C>G non_coding_transcript_exon_variant 0.14
rrl 1475366 n.1709G>A non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 0.99
katG 2154840 c.1272G>C synonymous_variant 0.98
PPE35 2168410 p.Thr735Ala missense_variant 1.0
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747468 p.Asp44Gly missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiB 3642316 p.Arg261Lys missense_variant 0.96
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 0.96
clpC1 4038744 p.Thr654Met missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
fbiC 1305494 c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant&stop_lost&splice_region_variant 1.0