TB-Profiler result

Run: ERR2653048
Summary

Run ID: ERR2653048

Sample name:

Date: 31-03-2023 22:27:58

Number of reads: 655930

Percentage reads mapped: 99.13

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 0.98
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 7582 p.Asp94Gly missense_variant 0.88 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.27 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288826 p.Val139Gly missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4248002 p.Gln497Lys 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
gyrB 5225 c.-15G>C upstream_gene_variant 0.12
gyrB 6438 p.Pro400Arg missense_variant 1.0
gyrA 7219 c.-83C>T upstream_gene_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 491071 p.Tyr97His missense_variant 0.1
fgd1 491591 p.Lys270Met missense_variant 0.94
mshA 575196 c.-152A>T upstream_gene_variant 0.12
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.15
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760629 c.823C>T synonymous_variant 0.12
rpoB 761152 p.Leu449Gln missense_variant 0.13
rpoB 761277 p.Ile491Leu missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765376 c.2007C>A synonymous_variant 0.12
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 1471891 n.46C>T non_coding_transcript_exon_variant 0.12
rrs 1472950 n.1105C>G non_coding_transcript_exon_variant 1.0
rrl 1475388 n.1731A>T non_coding_transcript_exon_variant 0.14
inhA 1674948 p.Trp249* stop_gained 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155219 p.Leu298Ser missense_variant 0.12
PPE35 2168001 p.Leu871Gln missense_variant 0.17
PPE35 2169017 p.Leu532Phe missense_variant 0.29
PPE35 2169053 c.1560T>C synonymous_variant 0.29
Rv1979c 2222149 p.Arg339Leu missense_variant 0.12
Rv1979c 2222665 p.Thr167Met missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289479 c.-238G>A upstream_gene_variant 0.12
pncA 2289548 c.-307C>T upstream_gene_variant 0.11
pncA 2289871 c.-630T>C upstream_gene_variant 0.12
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518955 p.Ala281Thr missense_variant 0.13
folC 2746822 p.Glu259Asp missense_variant 0.12
pepQ 2860584 c.-166C>G upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086896 c.79dupA frameshift_variant 0.2
ald 3087613 c.796delG frameshift_variant 0.46
Rv3083 3448689 c.186C>T synonymous_variant 0.11
Rv3083 3448965 c.464delG frameshift_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474731 p.Gly242Val missense_variant 0.13
whiB7 3568710 c.-31C>A upstream_gene_variant 0.15
fbiB 3640728 c.-807G>C upstream_gene_variant 0.18
fbiA 3640766 p.Pro75Leu missense_variant 0.14
fbiB 3642407 c.873C>T synonymous_variant 0.11
alr 3840472 p.Gly317Ser missense_variant 0.12
alr 3841061 c.360C>T synonymous_variant 0.11
rpoA 3878639 c.-132C>G upstream_gene_variant 0.11
clpC1 4038744 p.Thr654Met missense_variant 0.12
embC 4239935 p.Asn25Tyr missense_variant 0.15
embC 4240074 p.Glu71Gly missense_variant 0.14
embC 4241562 p.Arg567His missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4243122 p.Ser1087Ile missense_variant 0.18
aftB 4269792 c.-956C>A upstream_gene_variant 0.12
ethA 4326099 p.Gln459* stop_gained 1.0
ethA 4326441 p.Asn345Tyr missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0