TB-Profiler result

Run: SRR1175080
Summary

Run ID: SRR1175080

Sample name:

Date: 03-04-2023 03:37:27

Number of reads: 269836

Percentage reads mapped: 97.29

Strain: lineage4.3.3

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 761161 p.Leu452Pro missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288785 c.456dupC frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_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
gyrA 7315 p.Thr5Met missense_variant 0.33
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
rpoB 759893 c.87G>A synonymous_variant 0.33
rpoB 762889 p.His1028Arg missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777929 c.551delT frameshift_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800889 c.81C>A synonymous_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475502 n.1845A>G non_coding_transcript_exon_variant 0.2
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
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
pepQ 2860377 c.42C>A synonymous_variant 0.29
Rv2752c 3065671 p.Asp174Gly missense_variant 0.25
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640445 c.-98A>G upstream_gene_variant 0.29
embB 4249763 p.Thr1084Ser missense_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0