TB-Profiler result

Run: SRR22175193
Summary

Run ID: SRR22175193

Sample name:

Date: 04-04-2023 04:00:44

Number of reads: 7310695

Percentage reads mapped: 99.32

Strain: lineage2.2.1

Drug-resistance: 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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.31 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.4 rifampicin
mmpR5 779181 c.198dupG frameshift_variant 0.34 clofazimine, bedaquiline
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.64 isoniazid, ethionamide
fabG1 1673432 c.-8T>A upstream_gene_variant 0.36 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 0.61 pyrazinamide
pncA 2289228 p.Ile5Ser missense_variant 0.34 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.41 kanamycin
thyA 3074408 p.Thr22Ala missense_variant 0.4 para-aminosalicylic_acid
alr 3840393 p.Met343Thr missense_variant 0.45 cycloserine
embA 4243217 c.-16C>T upstream_gene_variant 0.41 ethambutol
embA 4243222 c.-11C>A upstream_gene_variant 0.55 ethambutol
embB 4247429 p.Met306Val missense_variant 0.65 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 491290 p.Val170Met missense_variant 0.39
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.37
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 766488 p.Pro1040Arg missense_variant 0.74
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
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
thyX 3067949 c.-4C>T upstream_gene_variant 0.34
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568442 p.Lys80Gln missense_variant 0.35
whiB7 3568443 p.His79Gln missense_variant 0.35
whiB7 3568854 c.-176delG upstream_gene_variant 0.7
Rv3236c 3612813 p.Thr102Ala missense_variant 0.99
embC 4241022 p.Ala387Val missense_variant 0.34
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247847 p.Gln445Arg missense_variant 0.38
aftB 4267647 p.Asp397Gly missense_variant 0.99
ethA 4326513 p.Thr321Pro missense_variant 0.66
ethA 4326676 p.Ser266Arg missense_variant 0.55
ethA 4327344 p.Thr44Pro missense_variant 0.37
whiB6 4338292 p.Ala77Val missense_variant 0.42
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.43
gid 4407927 p.Glu92Asp missense_variant 1.0