TB-Profiler result

Run: ERR4796657
Summary

Run ID: ERR4796657

Sample name:

Date: 01-04-2023 07:00:34

Number of reads: 3205735

Percentage reads mapped: 99.79

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.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
tlyA 1917991 p.Arg18* stop_gained 0.94 capreomycin
pncA 2289141 p.Tyr34Ser missense_variant 1.0 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
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
mshA 576108 p.Ala254Gly missense_variant 0.18
rpoB 759960 p.Thr52Pro missense_variant 0.16
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
katG 2155229 p.Gln295Lys missense_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.59
fbiD 3339744 c.627A>C synonymous_variant 0.2
fbiD 3339749 p.Val211Gly missense_variant 0.32
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
whiB7 3568428 c.250delG frameshift_variant 0.13
whiB7 3568840 c.-161A>G upstream_gene_variant 0.96
rpoA 3878609 c.-102T>G upstream_gene_variant 0.29
rpoA 3878639 c.-132C>G upstream_gene_variant 0.29
rpoA 3878641 c.-134C>G upstream_gene_variant 0.36
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.16
embB 4246555 c.42G>C synonymous_variant 0.14
embB 4246556 p.Ala15Pro missense_variant 0.14
embB 4246567 c.54G>T synonymous_variant 0.12
aftB 4268619 p.Val73Gly missense_variant 0.18
ethA 4327061 p.Ser138Ile missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408096 p.Val36Ala missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0