TB-Profiler result

Run: ERR2179657
Summary

Run ID: ERR2179657

Sample name:

Date: 10-08-2022 18:12:04

Number of reads: 2874113

Percentage reads mapped: 99.09

Strain: lineage4.4.2

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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.2 Euro-American T1;T2 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
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
katG 2156110 p.Val1Ala missense_variant 1.0 isoniazid
pncA 2288751 p.Ser164* stop_gained 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326994 c.479delC frameshift_variant 0.97 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 9304 p.Gly668Asp missense_variant 1.0
mshA 575906 p.Ala187Thr missense_variant 1.0
mshA 576462 c.1117dupG frameshift_variant 1.0
rpoC 767314 p.Tyr1315* stop_gained 0.42
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302914 c.-17A>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674952 p.Pro251Ala missense_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726146 c.-47_-46insT upstream_gene_variant 1.0
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448727 p.Leu75Arg missense_variant 1.0
Rv3083 3448783 p.Val94Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4039058 p.Phe549Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243991 c.759T>G synonymous_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 1.0
aftB 4267568 c.1269G>T synonymous_variant 1.0
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
whiB6 4338286 c.235delG frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338682 c.-161A>T upstream_gene_variant 1.0
gid 4407949 p.Asp85Val missense_variant 1.0