TB-Profiler result

Run: SRR14088386
Summary

Run ID: SRR14088386

Sample name:

Date: 03-04-2023 09:46:37

Number of reads: 1474190

Percentage reads mapped: 99.67

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 7570 p.Ala90Val missense_variant 0.18 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289057 p.Pro62Arg missense_variant 0.14 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
gid 4407830 p.Gln125* stop_gained 1.0 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
gyrB 5078 c.-162_-161insG upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7581 p.Asp94Thr missense_variant 0.19
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759692 c.-115T>A upstream_gene_variant 0.18
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765921 p.Ile851Thr missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778829 p.Gln26Arg missense_variant 0.14
mmpR5 779125 c.137dupG frameshift_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.4
rrl 1475089 n.1432A>G non_coding_transcript_exon_variant 1.0
rrl 1475838 n.2181T>A non_coding_transcript_exon_variant 0.67
fabG1 1673930 p.Ala164Asp missense_variant 0.12
rpsA 1833785 p.Val82Phe missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102024 p.Ala340Val missense_variant 1.0
katG 2154372 p.Asp580Glu missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155320 c.792G>A synonymous_variant 1.0
PPE35 2167725 p.Val963Ala missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168979 p.Pro545Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726750 c.558C>T synonymous_variant 0.11
Rv2752c 3065635 p.Pro186Leu missense_variant 0.12
thyA 3074648 c.-177T>G upstream_gene_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473820 c.-187C>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038660 p.Ser682Tyr missense_variant 0.12
clpC1 4038945 p.Asp587Val missense_variant 0.13
embC 4240009 c.147G>A synonymous_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246969 c.456T>C synonymous_variant 1.0
embB 4248004 p.Gln497His missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0