TB-Profiler result

Run: ERR6397154
Summary

Run ID: ERR6397154

Sample name:

Date: 02-04-2023 02:45:07

Number of reads: 3796367

Percentage reads mapped: 99.43

Strain: lineage4.2.2.2

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 0.98
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.97
lineage4.2.2.2 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 761155 p.Ser450Leu missense_variant 0.98 rifampicin
rpsL 781822 p.Lys88Thr missense_variant 0.98 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289036 p.Pro69Leu missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.99 ethambutol
gid 4407997 p.Gly69Asp missense_variant 0.93 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 0.97
mshA 576108 p.Ala254Gly missense_variant 0.19
rpoB 761489 c.1683G>A synonymous_variant 0.95
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
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.29
PPE35 2170053 p.Thr187Ser missense_variant 0.27
PPE35 2170065 p.Ala183Gly missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726146 c.-47_-46insT upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.98
ald 3086742 c.-78A>C upstream_gene_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.24
fbiD 3339744 c.627A>C synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878567 c.-60C>G upstream_gene_variant 0.12
rpoA 3878578 c.-71C>A upstream_gene_variant 0.17
rpoA 3878641 c.-134C>G upstream_gene_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.31
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.27
embB 4246556 p.Ala15Pro missense_variant 0.28
embB 4246563 p.Leu17Trp missense_variant 0.32
embB 4246567 c.54G>T synonymous_variant 0.32
ethA 4327472 c.2T>G start_lost 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0