TB-Profiler result

Run: ERR4829045

Summary

Run ID: ERR4829045

Sample name:

Date: 01-04-2023 19:14:51

Number of reads: 1150343

Percentage reads mapped: 99.64

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288821 c.419_420dupGC frameshift_variant 0.96 pyrazinamide
alr 3841409 p.Phe4Leu missense_variant 0.96 cycloserine
embB 4247431 p.Met306Ile missense_variant 0.94 ethambutol
ethA 4326174 c.1299dupG frameshift_variant 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
gyrB 6558 p.Gly440Ala missense_variant 0.15
gyrB 6944 p.Tyr569His missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.1
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 764529 p.Arg387His missense_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766487 p.Pro1040Ser missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461239 p.Phe65Leu missense_variant 0.17
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 0.27
PPE35 2170053 p.Thr187Ser missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518577 p.Gly155Cys missense_variant 0.11
folC 2746760 p.Gln280Arg missense_variant 0.11
Rv2752c 3064949 p.Val415Leu missense_variant 0.1
Rv2752c 3065865 c.326delT frameshift_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612424 c.693G>C synonymous_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244705 c.1473G>A synonymous_variant 0.11
ethA 4327379 p.Tyr32Cys missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0