TB-Profiler result

Run: SRR4035574
Summary

Run ID: SRR4035574

Sample name:

Date: 04-04-2023 07:11:16

Number of reads: 595193

Percentage reads mapped: 99.68

Strain: lineage4.3.4.2

Drug-resistance: HR-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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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
katG 2154254 c.1856_1857delTC frameshift_variant 0.15 isoniazid
ethA 4326712 c.761delA frameshift_variant 0.13 ethionamide
ethA 4326858 p.Gln206* stop_gained 0.25 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 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9586 c.2287dupG frameshift_variant 0.12
fgd1 491235 c.453C>T synonymous_variant 0.22
rpoB 759757 c.-50G>A upstream_gene_variant 0.17
rpoB 761385 p.Ala527Thr missense_variant 0.2
rpoB 762999 p.Met1065Val missense_variant 0.29
rpoC 763529 p.Pro54Thr missense_variant 0.12
rpoC 764185 c.816C>T synonymous_variant 0.14
rpoC 764405 c.1039delG frameshift_variant 0.22
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776205 p.Gly759Asp missense_variant 0.18
mmpL5 776585 c.1896C>T synonymous_variant 0.18
mmpS5 778914 c.-9C>T upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781676 c.117C>A synonymous_variant 0.12
rplC 800736 c.-73G>A upstream_gene_variant 0.1
fbiC 1302934 p.Pro2Ser missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.13
rrl 1476609 n.2952G>A non_coding_transcript_exon_variant 0.12
fabG1 1673627 p.Thr63Ile missense_variant 0.2
fabG1 1673899 p.Ala154Thr missense_variant 0.13
fabG1 1673915 p.Gly159Glu missense_variant 0.14
rpsA 1834247 c.707delA frameshift_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.3
PPE35 2169354 p.Gly420Asp missense_variant 0.12
PPE35 2169866 c.747G>C synonymous_variant 0.25
PPE35 2170549 p.Gly22Arg missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714411 p.Arg308Ser missense_variant 0.11
eis 2714423 p.Ala304Thr missense_variant 0.13
eis 2714443 p.Arg297His missense_variant 0.11
folC 2747608 c.-10C>T upstream_gene_variant 0.2
ribD 2987595 c.760delC frameshift_variant 0.17
Rv2752c 3065823 c.368delC frameshift_variant 0.14
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449365 p.Pro288Thr missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568815 c.-136G>A upstream_gene_variant 0.22
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiA 3640412 c.-131G>C upstream_gene_variant 0.12
fbiB 3642458 c.924G>A synonymous_variant 0.2
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039354 p.Arg451Cys missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.18
embA 4244421 p.Glu397Lys missense_variant 0.2
embB 4245854 c.-660C>T upstream_gene_variant 0.15
embB 4247000 p.Gly163Trp missense_variant 0.4
aftB 4268418 c.414_418dupCCTGG frameshift_variant 0.25
aftB 4268652 p.Ala62Val missense_variant 0.2
whiB6 4338477 c.45C>T synonymous_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407851 p.Arg118Cys missense_variant 0.17
gid 4408156 p.Leu16Arg missense_variant 1.0