TB-Profiler result

Run: ERR4796933
Summary

Run ID: ERR4796933

Sample name:

Date: 01-04-2023 07:17:32

Number of reads: 3645105

Percentage reads mapped: 99.63

Strain: lineage4.8

Drug-resistance: Pre-XDR-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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4327262 c.-924_211del frameshift_variant&start_lost 1.0 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 0.98
rpoB 761461 p.Arg552His 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 0.98
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168977 p.Ala546Thr missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.38
PPE35 2170053 p.Thr187Ser missense_variant 0.41
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.5
fbiD 3339745 p.Ala210Thr missense_variant 0.2
whiB7 3568428 c.252A>G synonymous_variant 0.23
clpC1 4039729 p.Asp326Asn missense_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.47
embB 4246548 p.Pro12Gln missense_variant 0.27
embB 4246555 c.42G>C synonymous_variant 0.22
embB 4246556 p.Ala15Pro missense_variant 0.22
embB 4246563 p.Leu17Trp missense_variant 0.2
embB 4246567 c.54G>T synonymous_variant 0.18
aftB 4268619 p.Val73Gly missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0