TB-Profiler result

Run: ERR2515528
Summary

Run ID: ERR2515528

Sample name:

Date: 31-03-2023 20:58:55

Number of reads: 922841

Percentage reads mapped: 99.79

Strain: lineage4.9.1

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
lineage4.9 Euro-American (H37Rv-like) T1 None 1.0
lineage4.9.1 Euro-American (H37Rv-like) T1 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 0.17 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288776 c.464_465dupTG frameshift_variant 0.17 pyrazinamide
pncA 2288820 p.Gln141Pro missense_variant 0.77 pyrazinamide
embB 4247728 p.Glu405Asp missense_variant 1.0 ethambutol
ethA 4326721 c.752dupG frameshift_variant 0.76 ethionamide, 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 7567 p.Asp89Gly missense_variant 0.83
gyrA 8978 c.1677C>T synonymous_variant 1.0
fgd1 491310 c.528C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304849 p.Asn640Thr missense_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289138 p.Leu35Arg missense_variant 1.0
Rv2752c 3064543 p.Met550Thr missense_variant 0.11
fbiD 3339385 p.Asp90Asn missense_variant 1.0
Rv3083 3449820 c.1317G>C synonymous_variant 1.0
embA 4243200 c.-32delG upstream_gene_variant 1.0
ethA 4326925 p.Ser183Arg missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0