TB-Profiler result

Run: ERR2516502
Summary

Run ID: ERR2516502

Sample name:

Date: 31-03-2023 21:34:49

Number of reads: 8336923

Percentage reads mapped: 99.76

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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.Ser450Trp missense_variant 1.0 rifampicin
fabG1 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
katG 2154412 p.Phe567Ser missense_variant 1.0 isoniazid
pncA 2289054 p.Asp63Ala missense_variant 0.35 pyrazinamide
pncA 2289150 p.Ile31Ser missense_variant 0.73 pyrazinamide
embA 4243221 c.-12C>T upstream_gene_variant 0.34 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.64 ethambutol
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
gid 4408100 c.102delG frameshift_variant 1.0 streptomycin
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
ccsA 620475 c.585G>A synonymous_variant 1.0
rpoB 762391 p.Leu862Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918745 c.806A>G stop_lost&splice_region_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289656 c.-415C>A upstream_gene_variant 1.0
folC 2747612 c.-14T>G upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.24
ald 3087095 c.276C>T synonymous_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245899 c.-615C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338632 c.-112_-111insTTAACAGG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0