TB-Profiler result

Run: ERR4797311
Summary

Run ID: ERR4797311

Sample name:

Date: 01-04-2023 07:33:20

Number of reads: 4826453

Percentage reads mapped: 99.61

Strain: lineage3;lineage2.2.1.1

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 0.51
lineage2 East-Asian Beijing RD105 0.48
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.46
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.51
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.45
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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Pro missense_variant 0.48 rifampicin
rpoB 761110 p.Asp435Gly missense_variant 0.49 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.52 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.47 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.48 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 0.5 pyrazinamide
pncA 2289206 p.Asp12Glu missense_variant 0.42 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.64 ethambutol
embB 4247513 p.Tyr334His missense_variant 0.31 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.47 ethambutol
ethA 4326321 c.1152dupT frameshift_variant 0.61 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
mshA 575907 p.Ala187Val missense_variant 0.46
mshA 576108 p.Ala254Gly missense_variant 0.28
ccsA 620625 p.Ile245Met missense_variant 0.45
rpoB 759746 c.-61C>T upstream_gene_variant 0.6
rpoC 762434 c.-936T>G upstream_gene_variant 0.57
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766466 p.Glu1033Lys missense_variant 0.63
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.6
mmpR5 779130 c.144dupC frameshift_variant 0.55
mmpS5 779615 c.-710C>G upstream_gene_variant 0.6
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.55
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472504 n.659A>G non_coding_transcript_exon_variant 0.22
rrl 1475378 n.1721A>G non_coding_transcript_exon_variant 0.18
rrl 1475477 n.1820A>G non_coding_transcript_exon_variant 0.15
inhA 1673406 c.-796C>T upstream_gene_variant 0.33
rpsA 1834177 c.636A>C synonymous_variant 0.49
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.97
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222700 c.465C>T synonymous_variant 0.61
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.45
pncA 2289365 c.-125delC upstream_gene_variant 0.46
eis 2714846 p.Val163Ile missense_variant 0.44
ahpC 2726105 c.-88G>A upstream_gene_variant 0.54
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.58
alr 3841473 c.-53G>A upstream_gene_variant 0.63
embC 4242075 p.Arg738Gln missense_variant 0.55
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.56
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4247880 p.Val456Ala missense_variant 0.61
embB 4248115 c.1602C>T synonymous_variant 0.54
aftB 4267492 p.Ala449Thr missense_variant 0.55
aftB 4267647 p.Asp397Gly missense_variant 0.45
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.42
gid 4407967 p.Leu79Trp missense_variant 0.7