TB-Profiler result

Run: ERR2516503
Summary

Run ID: ERR2516503

Sample name:

Date: 31-03-2023 21:34:31

Number of reads: 2898212

Percentage reads mapped: 99.69

Strain: lineage4

Drug-resistance: 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
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 7521 p.Ala74Ser missense_variant 0.41 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.4 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
mmpR5 779181 c.198dupG frameshift_variant 0.98 clofazimine, bedaquiline
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288703 p.Val180Gly missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 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 9304 p.Gly668Asp missense_variant 1.0
mshA 575837 c.490C>T synonymous_variant 1.0
mshA 575910 c.565delG frameshift_variant 0.98
mshA 575932 c.587dupC frameshift_variant 1.0
rpoB 761889 p.Val695Leu missense_variant 1.0
rpoC 766487 p.Pro1040Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777875 c.605delG frameshift_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801009 c.201A>G synonymous_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101831 c.1212G>A synonymous_variant 1.0
katG 2156173 c.-62C>A upstream_gene_variant 0.99
PPE35 2169866 c.747G>C synonymous_variant 0.25
Rv1979c 2223214 c.-50A>C upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726141 c.-52C>A upstream_gene_variant 1.0
Rv2752c 3065517 c.675C>T synonymous_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.22
thyA 3074495 c.-24C>T upstream_gene_variant 1.0
Rv3083 3448679 c.177dupG frameshift_variant 0.46
fprA 3474299 p.Asp98Gly missense_variant 1.0
Rv3236c 3612219 p.Val300Ile missense_variant 1.0
rpoA 3878580 c.-74_-73insCAACCCA upstream_gene_variant 0.4
rpoA 3878595 c.-88C>T upstream_gene_variant 0.53
rpoA 3878635 c.-128C>T upstream_gene_variant 0.21
clpC1 4038857 c.1848C>A synonymous_variant 0.2
embC 4242425 p.Arg855Gly missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326632 p.His281Arg missense_variant 0.26
ethA 4326771 p.Tyr235Asp missense_variant 0.54
ethA 4328317 c.-844C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407967 p.Leu79Trp missense_variant 1.0