TB-Profiler result

Run: SRR3105791
Summary

Run ID: SRR3105791

Sample name:

Date: 04-04-2023 05:09:44

Number of reads: 2390824

Percentage reads mapped: 99.04

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 0.94
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
gyrB 6738 p.Thr500Asn missense_variant 0.93 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Pro missense_variant 0.94 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.12 streptomycin
inhA 1674048 c.-154G>A upstream_gene_variant 0.83 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 0.12 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.87 isoniazid
pncA 2288718 p.Met175Arg missense_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.82 ethambutol
ethA 4326798 c.675dupC frameshift_variant 0.82 ethionamide
pncA 2285268 c.-145_*3412del transcript_ablation 1.0 pyrazinamide
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 5081 c.-159_-158insA upstream_gene_variant 0.92
gyrB 6240 p.Asp334Gly missense_variant 0.88
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 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.92
rpoC 762434 c.-936T>G upstream_gene_variant 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
rpoC 767314 p.Tyr1315* stop_gained 0.28
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674952 p.Pro251Ala missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918404 c.465G>A synonymous_variant 0.94
katG 2154102 c.2010C>T synonymous_variant 0.9
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168863 c.1750C>T synonymous_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.67
pncA 2289622 c.-382delA upstream_gene_variant 0.96
kasA 2518132 c.18C>T synonymous_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 0.17
ahpC 2726105 c.-88G>A upstream_gene_variant 0.9
Rv2752c 3065163 c.1029C>G synonymous_variant 0.9
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568689 c.-10G>A upstream_gene_variant 0.96
alr 3841356 p.Ser22Leu missense_variant 0.91
rpoA 3878641 c.-135delG upstream_gene_variant 0.29
embC 4242075 p.Arg738Gln missense_variant 0.95
embC 4242425 p.Arg855Gly missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.17
ubiA 4269031 p.Gly268Asp missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407966 p.Leu79Phe missense_variant 0.81