TB-Profiler result

Run: ERR2516575
Summary

Run ID: ERR2516575

Sample name:

Date: 31-03-2023 21:37:01

Number of reads: 1534068

Percentage reads mapped: 99.34

Strain: lineage4.2.2.1

Drug-resistance: MDR-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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
lineage4.2.2.1 Euro-American LAM7-TUR 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
folC 2747141 p.Glu153Ala missense_variant 1.0 para-aminosalicylic_acid
embB 4248002 p.Gln497Lys missense_variant 1.0 ethambutol
ethA 4326419 c.1054delG frameshift_variant 1.0 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491166 c.384G>A synonymous_variant 0.13
mshA 576077 c.730C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778394 c.-596A>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917953 p.Ala5Val missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102172 p.Glu291Lys missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.32
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.3
ald 3086742 c.-78A>C upstream_gene_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449359 p.Phe286Leu missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878518 c.-11G>T upstream_gene_variant 0.15
clpC1 4038857 c.1848C>A synonymous_variant 0.5
embC 4241094 p.Cys411Tyr missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407847 p.Ala119Asp missense_variant 1.0