TB-Profiler result

Run: SRR1140575
Summary

Run ID: SRR1140575

Sample name:

Date: 02-04-2023 20:56:20

Number of reads: 3146053

Percentage reads mapped: 99.44

Strain: lineage3;lineage2.2.1

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 0.43
lineage2 East-Asian Beijing RD105 0.59
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.63
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.54
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.Asp94Ala missense_variant 0.51 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.24 rifampicin
katG 2155700 p.Asn138His missense_variant 0.52 isoniazid
embB 4249518 p.His1002Arg missense_variant 0.41 ethambutol
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 0.58
ccsA 620625 p.Ile245Met missense_variant 0.68
rpoB 759746 c.-61C>T upstream_gene_variant 0.25
rpoB 761292 p.Val496Met missense_variant 0.42
rpoC 762434 c.-936T>G upstream_gene_variant 0.4
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.69
mmpS5 779615 c.-710C>G upstream_gene_variant 0.62
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.74
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.52
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.46
eis 2714526 c.805_806delAC frameshift_variant 0.67
ahpC 2726105 c.-88G>A upstream_gene_variant 0.35
ahpC 2726117 c.-76T>A upstream_gene_variant 0.43
Rv2752c 3065711 p.Gly161Ser missense_variant 0.49
ald 3086788 c.-32T>C upstream_gene_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.64
fbiB 3642877 p.Lys448Arg missense_variant 0.37
embC 4240767 p.Arg302Leu missense_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.57
aftB 4267647 p.Asp397Gly missense_variant 0.57
whiB6 4338329 p.Asp65Tyr missense_variant 0.56
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.55