TB-Profiler result

Run: ERR4423565
Summary

Run ID: ERR4423565

Sample name:

Date: 01-04-2023 05:53:40

Number of reads: 984704

Percentage reads mapped: 99.61

Strain: lineage4.1.1.3

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
lineage4.1 Euro-American T;X;H None 0.89
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.89
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.93
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.Asp94Gly missense_variant 0.91 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.94 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.88 streptomycin
katG 2155167 p.Ser315Thr missense_variant 0.8 isoniazid
pncA 2288827 p.Val139Met missense_variant 0.85 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 0.94 isoniazid
embB 4247429 p.Met306Val missense_variant 0.79 ethambutol
ethA 4326876 c.597delC frameshift_variant 0.94 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
gyrB 5520 p.Pro94Leu missense_variant 0.14
gyrB 6608 p.Val457Leu missense_variant 0.88
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 0.93
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801354 c.546G>A synonymous_variant 0.91
inhA 1674320 p.Gly40Val missense_variant 0.12
rpsA 1834045 p.Glu168Asp missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156359 c.-248C>A upstream_gene_variant 0.12
PPE35 2168080 p.Thr845Ala missense_variant 0.29
PPE35 2168839 p.Pro592Thr missense_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065610 c.582C>A synonymous_variant 0.15
thyA 3074378 p.Gln32Lys missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087192 p.Gly125Ser missense_variant 0.12
Rv3083 3449616 p.Met371Ile missense_variant 0.95
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877949 p.Thr187Ala missense_variant 0.93
clpC1 4038287 c.2418C>T synonymous_variant 0.12
clpC1 4038695 c.2010C>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.89
embB 4249408 c.2895G>A synonymous_variant 0.93
aftB 4267104 p.Val578Ala missense_variant 0.12
ethA 4326213 c.1261C>A synonymous_variant 0.17
ethR 4327564 p.Ala6Ser missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0