TB-Profiler result

Run: SRR7592389
Summary

Run ID: SRR7592389

Sample name:

Date: 04-04-2023 19:51:41

Number of reads: 2935801

Percentage reads mapped: 99.49

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 7581 p.Asp94Tyr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288805 p.Ala146Val missense_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
ethA 4326801 c.672dupG frameshift_variant 0.26 ethionamide, ethionamide
gid 4407830 p.Gln125* stop_gained 1.0 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
rpoC 764817 p.Val483Ala missense_variant 1.0
rpoC 765008 p.Leu547Val missense_variant 1.0
rpoC 766085 p.Pro906Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460992 c.-53A>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
fabG1 1673553 p.Asp38Glu missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.13
PPE35 2169910 p.Asn235Tyr missense_variant 0.13
PPE35 2170065 p.Ala183Gly missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.16
ald 3086863 p.Arg15Gln missense_variant 0.69
ald 3087849 c.1031dupC frameshift_variant 0.18
fbiD 3339734 p.Ala206Gly missense_variant 0.54
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
alr 3840764 c.657G>C synonymous_variant 1.0
rpoA 3878618 c.-111A>C upstream_gene_variant 0.12
rpoA 3878641 c.-134C>G upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.5
embB 4246548 p.Pro12Gln missense_variant 0.5
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246584 p.Arg24Pro missense_variant 0.5
ethA 4326078 c.1393_1395dupATC conservative_inframe_insertion 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0