TB-Profiler result

Run: SRR1175057

Summary

Run ID: SRR1175057

Sample name:

Date: 03-04-2023 03:37:02

Number of reads: 306556

Percentage reads mapped: 95.56

Strain: lineage4.3

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 0.98
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 1.0 rifampicin
rrs 1472753 n.908A>G non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 1.0 ethionamide
pncA 2288565 c.377_*115del frameshift_variant&stop_lost&splice_region_variant 1.0 pyrazinamide
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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9501 p.Arg734Ser missense_variant 0.4
fgd1 491625 c.843C>T synonymous_variant 0.22
mshA 576274 c.927G>T synonymous_variant 0.15
rpoB 761547 p.Val581Met missense_variant 0.9
rpoC 763067 c.-303C>G upstream_gene_variant 0.4
rpoC 763070 c.-300T>C upstream_gene_variant 0.4
rpoC 763085 c.-285C>G upstream_gene_variant 0.4
rpoC 763115 c.-255T>C upstream_gene_variant 0.33
rpoC 763136 c.-234C>T upstream_gene_variant 0.22
rpoC 763148 c.-222G>C upstream_gene_variant 0.22
rpoC 763158 c.-212C>T upstream_gene_variant 0.22
rpoC 763166 c.-204A>G upstream_gene_variant 0.22
rpoC 763807 c.438T>C synonymous_variant 0.4
rpoC 763816 c.447C>G synonymous_variant 0.33
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475640 n.1983G>A non_coding_transcript_exon_variant 0.13
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
rpsA 1833811 c.270G>T synonymous_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103109 c.-67C>T upstream_gene_variant 0.33
PPE35 2169320 p.Leu431Phe missense_variant 0.25
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
Rv2752c 3067065 c.-874G>T upstream_gene_variant 0.25
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449776 p.Asp425Tyr missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475093 p.Gly363Arg missense_variant 0.22
alr 3841461 c.-41C>A upstream_gene_variant 0.29
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242115 c.2253G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245357 p.Ala709Ser missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4407912 c.160_290del frameshift_variant 1.0