TB-Profiler result

Run: SRR1103491

Summary

Run ID: SRR1103491

Sample name:

Date: 02-04-2023 20:43:27

Number of reads: 709527

Percentage reads mapped: 46.35

Strain: lineage4

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
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
rpoC 765609 p.Asp747Ala missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4407796 p.Ser136* stop_gained 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
mshA 575562 p.Met72Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777727 p.Phe252Val missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407278 c.63G>T synonymous_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918740 c.801C>A synonymous_variant 0.3
katG 2154980 c.1132C>T synonymous_variant 1.0
PPE35 2170030 p.Met195Leu missense_variant 0.4
PPE35 2170596 p.Leu6Ser missense_variant 1.0
PPE35 2170811 c.-199C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746174 c.1425A>C synonymous_variant 0.25
pepQ 2859594 c.825T>G synonymous_variant 0.33
Rv2752c 3065473 p.Ser240Tyr missense_variant 0.12
ald 3087211 p.Ala131Val missense_variant 0.25
Rv3083 3449145 c.642G>A synonymous_variant 1.0
fprA 3475209 p.Asp401Glu missense_variant 0.29
fbiB 3641535 c.1T>G start_lost 0.4
alr 3840368 c.1053C>A synonymous_variant 0.17
rpoA 3877515 c.993G>A synonymous_variant 0.12
rpoA 3878525 c.-18A>C upstream_gene_variant 0.6
embB 4247821 c.1308T>G synonymous_variant 0.4
aftB 4268076 p.Met254Ala missense_variant 1.0
ethA 4327004 p.Phe157Cys missense_variant 0.33
ethA 4327022 p.Phe151Cys missense_variant 0.33
whiB6 4338479 p.Phe15Val missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0