TB-Profiler result

Run: ERR5897097

Summary

Run ID: ERR5897097

Sample name:

Date: 02-04-2023 00:49:26

Number of reads: 7897892

Percentage reads mapped: 99.39

Strain: lineage4.6.2.1;lineage3

Drug-resistance: MDR-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
lineage3 East-African-Indian CAS RD750 0.12
lineage4 Euro-American LAM;T;S;X;H None 0.88
lineage4.6 Euro-American T;LAM None 0.89
lineage4.6.2 Euro-American T;LAM RD726 0.87
lineage4.6.2.1 Euro-American T3 RD726 0.89
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
rpoB 761140 p.His445Arg missense_variant 0.89 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.12 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.14 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.1 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288883 p.Leu120Arg missense_variant 0.12 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
gid 4407851 c.351delG frameshift_variant 0.84 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
gyrA 7581 p.Asp94Ser missense_variant 0.84
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.12
mmpR5 778298 c.-692C>T upstream_gene_variant 0.91
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918272 c.333C>T synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 0.16
Rv1979c 2221882 p.Leu428Gln missense_variant 0.82
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.14
pncA 2289365 c.-125delC upstream_gene_variant 0.12
eis 2714606 p.Ala243Ser missense_variant 0.89
ahpC 2726105 c.-88G>A upstream_gene_variant 0.17
ahpC 2726600 c.408T>C synonymous_variant 0.8
ald 3086788 c.-32T>C upstream_gene_variant 0.15
fbiD 3338919 c.-199C>G upstream_gene_variant 0.86
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 0.13
rpoA 3878601 c.-95delG upstream_gene_variant 0.27
rpoA 3878613 c.-113_-107delCAACCCA upstream_gene_variant 0.19
rpoA 3878654 c.-147A>G upstream_gene_variant 0.83
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242883 c.-350C>T upstream_gene_variant 0.91
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.15
gid 4407790 p.Ala138Val missense_variant 0.14