TB-Profiler result

Run: ERR2179637
Summary

Run ID: ERR2179637

Sample name:

Date: 15-08-2022 12:00:27

Number of reads: 2717952

Percentage reads mapped: 98.96

Strain: lineage4.2.2

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
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 761140 p.His445Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 576077 c.730C>T synonymous_variant 1.0
rpoC 765584 p.Pro739Ser missense_variant 1.0
rpoC 767314 p.Tyr1315* stop_gained 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 778748 p.Pro53Leu missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674952 p.Pro251Ala missense_variant 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611957 c.1154_*1delACTAGG frameshift_variant&stop_lost&splice_region_variant 1.0
Rv3236c 3611965 c.1152G>C synonymous_variant 1.0
Rv3236c 3612469 c.648A>G synonymous_variant 1.0
alr 3841567 c.-147A>G upstream_gene_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.28
embC 4240228 c.366G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407797 p.Ser136Pro missense_variant 1.0