TB-Profiler result

Run: ERR2510289
Summary

Run ID: ERR2510289

Sample name:

Date: 31-03-2023 18:39:23

Number of reads: 746200

Percentage reads mapped: 99.58

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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673432 c.-8T>G upstream_gene_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 1.0 pyrazinamide
embA 4243222 c.-11C>A upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4327032 c.440_441dupAC frameshift_variant 1.0 ethionamide, 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 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761892 p.Ile696Val missense_variant 0.17
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763074 p.Thr1090Ala missense_variant 0.12
rpoC 765762 p.Pro798Leu missense_variant 0.2
rpoC 767123 p.Val1252Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407478 c.-138C>T upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472567 n.722G>T non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168140 p.Ala825Thr missense_variant 0.11
PPE35 2168150 c.2463T>C synonymous_variant 0.11
PPE35 2169091 p.Val508Leu missense_variant 0.33
PPE35 2169655 p.Gly320* stop_gained 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.54
PPE35 2170053 p.Thr187Ser missense_variant 0.5
Rv1979c 2222602 p.Gln188Arg missense_variant 0.17
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
pncA 2290097 c.-856T>C upstream_gene_variant 0.13
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747321 p.Thr93Ser missense_variant 0.14
folC 2747325 p.Arg92Cys missense_variant 0.12
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449041 p.Val180Phe missense_variant 0.22
Rv3083 3449593 p.Glu364Lys missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641369 p.Tyr276Cys missense_variant 0.1
alr 3841037 c.384G>A synonymous_variant 0.15
alr 3841473 c.-53G>A upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248550 c.2037C>T synonymous_variant 0.12
embB 4249564 p.Asp1017Glu missense_variant 1.0
aftB 4267895 p.Phe314Leu missense_variant 0.38
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0