TB-Profiler result

Run: SRR857286
Summary

Run ID: SRR857286

Sample name:

Date: 04-04-2023 21:29:16

Number of reads: 4169898

Percentage reads mapped: 99.53

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 Euro-American (LAM) mainly-LAM None 0.99
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 761109 p.Asp435Tyr 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 2288847 p.Gly132Ala missense_variant 1.0 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 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 759831 p.Thr9Pro missense_variant 0.22
rpoB 761266 p.Asn487Ser missense_variant 0.99
rpoB 762249 p.Leu815Val missense_variant 0.19
rpoC 762836 c.-534C>G upstream_gene_variant 0.62
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
fabG1 1673449 p.Thr4Pro missense_variant 0.56
inhA 1674892 p.Asn231Asp missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.17
PPE35 2169866 c.747G>C synonymous_variant 0.18
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
ahpC 2726756 c.564C>G synonymous_variant 0.23
Rv2752c 3064552 p.Arg547Pro missense_variant 0.27
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611982 p.Ala379Pro missense_variant 0.12
fbiB 3641955 p.Gly141Arg missense_variant 0.29
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039932 p.Gly258Val missense_variant 0.28
embC 4241429 p.Phe523Val missense_variant 0.36
embC 4242476 p.Pro872Ala missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.34
embB 4248725 p.Ser738Ala missense_variant 0.31
ubiA 4269529 p.Ala102Gly missense_variant 0.27
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407922 p.Leu94Gln missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4407912 c.160_290del frameshift_variant 1.0