TB-Profiler result

Run: ERR1213872

Summary

Run ID: ERR1213872

Sample name:

Date: 11-08-2022 20:25:51

Number of reads: 2564119

Percentage reads mapped: 99.26

Strain: lineage4.3.3

Drug-resistance: Pre-XDR-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 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
gyrA 7582 p.Asp94Ala missense_variant 0.96 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.97 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674248 p.Ile16Thr missense_variant 1.0 isoniazid
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.96 ethambutol
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 0.98
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761315 c.1510_1512dupGGG conservative_inframe_insertion 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.97
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 0.97
tlyA 1917972 c.33A>G synonymous_variant 0.94
katG 2155012 p.Pro367Leu missense_variant 0.98
PPE35 2169866 c.747G>C synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
ribD 2987307 p.Ala157Pro missense_variant 0.15
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
clpC1 4038287 c.2418C>T synonymous_variant 1.0
panD 4044437 c.-156C>T upstream_gene_variant 0.18
embC 4241436 p.Ala525Asp missense_variant 0.27
embC 4242425 p.Arg855Gly missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243770 p.Gly180Arg missense_variant 0.12
embA 4246322 p.Phe1030Leu missense_variant 1.0
aftB 4268411 c.426G>A synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408102 p.Gly34Glu missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0