TB-Profiler result

Run: ERR369667
Summary

Run ID: ERR369667

Sample name:

Date: 01-04-2023 02:48:26

Number of reads: 3997803

Percentage reads mapped: 99.45

Strain: lineage4.6.2.2;lineage3

Drug-resistance: HR-TB

Download CSV Download TXT Download PDF Download JSON
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 0.87
lineage4 Euro-American LAM;T;S;X;H None 0.15
lineage4.6 Euro-American T;LAM None 0.13
lineage4.6.2 Euro-American T;LAM RD726 0.17
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 0.14
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
fabG1 1673425 c.-15C>T upstream_gene_variant 0.23 isoniazid, 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
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 491742 c.960T>C synonymous_variant 0.8
rpoB 759746 c.-61C>T upstream_gene_variant 0.84
rpoC 762434 c.-936T>G upstream_gene_variant 0.88
rpoC 763031 c.-339T>C upstream_gene_variant 0.83
rpoC 766582 c.3213C>A synonymous_variant 0.81
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.86
mmpR5 778298 c.-692C>T upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472487 n.643dupT non_coding_transcript_exon_variant 0.17
rpsA 1833979 c.438T>C synonymous_variant 0.81
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.83
katG 2155389 c.723C>G synonymous_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 0.8
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.85
pncA 2289365 c.-125delC upstream_gene_variant 0.8
ahpC 2726105 c.-88G>A upstream_gene_variant 0.81
ahpC 2726338 p.Val49Gly missense_variant 0.3
thyX 3067474 p.Pro158Ala missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 0.92
Rv3083 3448567 p.His22Asp missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 0.15
Rv3236c 3612910 p.Leu69Phe missense_variant 0.18
alr 3841473 c.-53G>A upstream_gene_variant 0.78
clpC1 4038857 c.1848C>A synonymous_variant 0.21
embC 4242075 p.Arg738Gln missense_variant 0.83
embA 4242550 c.-683C>G upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4267272 p.Lys522Arg missense_variant 0.19
ethR 4326739 c.-810G>C upstream_gene_variant 0.18
ethA 4328004 c.-531C>T upstream_gene_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.85