TB-Profiler result

Run: ERR4799172
Summary

Run ID: ERR4799172

Sample name:

Date: 01-04-2023 08:55:24

Number of reads: 3168331

Percentage reads mapped: 99.68

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 0.98
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 7581 p.Asp94His missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288850 c.391dupG frameshift_variant 0.98 pyrazinamide, pyrazinamide
embB 4249518 p.His1002Arg missense_variant 0.96 ethambutol
ethA 4326818 c.655dupG frameshift_variant 0.12 ethionamide
ethA 4326922 c.550_551dupGG frameshift_variant 0.8 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 1.0
mshA 576108 p.Ala254Gly missense_variant 0.27
mshA 576482 p.Val379Leu missense_variant 0.13
rpoC 764669 p.Pro434Thr missense_variant 0.85
rpoC 764817 p.Val483Ala missense_variant 0.1
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
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 0.98
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289969 c.-728G>C upstream_gene_variant 1.0
ald 3087647 c.830dupG frameshift_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.6
rpoA 3878641 c.-134C>G upstream_gene_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246542 p.Ser10Asn missense_variant 0.22
embB 4246584 p.Arg24Pro missense_variant 0.5
embB 4247028 p.Leu172Arg missense_variant 0.17
ubiA 4269124 p.Ala237Val missense_variant 0.97
ethR 4326844 c.-705G>C upstream_gene_variant 0.99
whiB6 4338362 p.Arg54Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408061 p.His48Asn missense_variant 0.99
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0