TB-Profiler result

Run: SRR22175239
Summary

Run ID: SRR22175239

Sample name:

Date: 04-04-2023 04:02:48

Number of reads: 5457957

Percentage reads mapped: 99.53

Strain: lineage3.1.2;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
lineage3 East-African-Indian CAS RD750 0.28
lineage2 East-Asian Beijing RD105 0.7
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.71
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.35
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.33
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.68
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 0.59 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.4 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.59 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.35 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.62 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.73 rifampicin
mmpR5 779181 c.198dupG frameshift_variant 0.74 clofazimine, bedaquiline
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673432 c.-8T>A upstream_gene_variant 0.7 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289228 p.Ile5Ser missense_variant 0.76 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.75 kanamycin
thyA 3074408 p.Thr22Ala missense_variant 0.6 para-aminosalicylic_acid
alr 3840393 p.Met343Thr missense_variant 0.67 cycloserine
embA 4243217 c.-16C>T upstream_gene_variant 0.67 ethambutol
embB 4247469 p.Tyr319Ser missense_variant 0.32 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 0.62
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.69
ccsA 620625 p.Ile245Met missense_variant 0.58
rpoB 759746 c.-61C>T upstream_gene_variant 0.35
rpoC 762434 c.-936T>G upstream_gene_variant 0.35
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 0.72
mmpS5 779615 c.-710C>G upstream_gene_variant 0.72
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406242 p.Ala367Thr missense_variant 0.31
Rv1258c 1406760 c.580_581insC frameshift_variant 0.7
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.66
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 0.24
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.34
pncA 2289054 p.Asp63Val missense_variant 0.34
pncA 2289365 c.-125delC upstream_gene_variant 0.36
ahpC 2726105 c.-88G>A upstream_gene_variant 0.29
thyX 3067949 c.-4C>T upstream_gene_variant 0.7
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
Rv3236c 3612813 p.Thr102Ala missense_variant 0.67
alr 3840626 c.795C>T synonymous_variant 0.28
embC 4241022 p.Ala387Val missense_variant 0.65
embC 4242075 p.Arg738Gln missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4243460 c.228C>T synonymous_variant 0.74
embB 4247847 p.Gln445Arg missense_variant 0.73
aftB 4267647 p.Asp397Gly missense_variant 0.68
ethA 4327344 p.Thr44Pro missense_variant 0.58
whiB6 4338292 p.Ala77Val missense_variant 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407620 p.Tyr195His missense_variant 0.57
gid 4407927 p.Glu92Asp missense_variant 0.74