TB-Profiler result

Run: SRR1174308
Summary

Run ID: SRR1174308

Sample name:

Date: 03-04-2023 03:34:13

Number of reads: 1247230

Percentage reads mapped: 97.91

Strain: 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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 0.95 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 1.0 streptomycin
tlyA 1918137 c.201_202dupGC frameshift_variant 0.4 capreomycin, capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288805 p.Ala146Glu missense_variant 1.0 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
embB 4247574 p.Asp354Ala missense_variant 1.0 ethambutol
ethA 4327480 c.-7T>C upstream_gene_variant 1.0 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 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765846 p.Asn826Thr missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_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 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303539 c.609G>A synonymous_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673284 c.-156G>T upstream_gene_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917769 c.-171C>G upstream_gene_variant 0.17
tlyA 1917822 c.-118G>A upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918594 p.Gly219Ser missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169320 p.Leu431Phe missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518582 c.468G>C synonymous_variant 0.15
kasA 2518587 p.Leu158His missense_variant 0.15
kasA 2518717 c.603C>A synonymous_variant 0.12
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
Rv2752c 3064875 c.1317C>A synonymous_variant 0.11
thyX 3067576 p.Asp124Asn missense_variant 0.12
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 1.0
panD 4044307 c.-26A>C upstream_gene_variant 0.12
embC 4239696 c.-167C>T upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243118 p.Trp1086Arg missense_variant 0.12
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244477 c.1245G>A synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338563 c.-42G>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0