TB-Profiler result

Run: ERR4799570

Summary

Run ID: ERR4799570

Sample name:

Date: 20-10-2023 03:30:58

Number of reads: 3109465

Percentage reads mapped: 99.65

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
Rifampicin R rpoB p.Gln432Pro (0.59)
Isoniazid R fabG1 c.-15C>T (0.56), katG p.Ser315Thr (0.91)
Ethambutol R embA c.-16C>T (0.36)
Pyrazinamide R pncA p.Ile5Ser (0.31)
Streptomycin R rpsL p.Lys43Arg (0.35)
Fluoroquinolones R gyrA p.Ala90Val (0.28)
Moxifloxacin R gyrA p.Ala90Val (0.28)
Ofloxacin R gyrA p.Ala90Val (0.28)
Levofloxacin R gyrA p.Ala90Val (0.28)
Ciprofloxacin R gyrA p.Ala90Val (0.28)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-10G>A (0.38)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.56), ethA p.Gln206* (0.29)
Clofazimine
Para-aminosalicylic_acid R thyA p.Thr22Ala (0.27)
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.62
lineage2 East-Asian Beijing RD105 0.37
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.37
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.38
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 0.28 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761101 p.Gln432Pro missense_variant 0.59 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.35 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.56 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.91 isoniazid
pncA 2289228 p.Ile5Ser missense_variant 0.31 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.38 kanamycin
thyA 3074408 p.Thr22Ala missense_variant 0.27 para-aminosalicylic_acid
embA 4243217 c.-16C>T upstream_gene_variant 0.36 ethambutol
ethA 4326858 p.Gln206* stop_gained 0.29 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 491290 p.Val170Met missense_variant 0.36
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.37
ccsA 620625 p.Ile245Met missense_variant 0.46
rpoB 759746 c.-61C>T upstream_gene_variant 0.76
rpoC 762434 c.-936T>G upstream_gene_variant 0.61
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764669 p.Pro434Thr missense_variant 0.54
rpoC 764703 p.Lys445Arg missense_variant 0.32
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.98
mmpL5 776182 p.Asp767Asn missense_variant 0.36
mmpS5 779615 c.-710C>G upstream_gene_variant 0.36
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303174 p.Leu82Val missense_variant 0.58
Rv1258c 1406760 c.580_581insC frameshift_variant 0.46
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.34
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.66
pncA 2289365 c.-125delC upstream_gene_variant 0.7
kasA 2518126 c.12T>C synonymous_variant 0.55
ahpC 2726105 c.-88G>A upstream_gene_variant 0.46
thyX 3067949 c.-4C>T upstream_gene_variant 0.28
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 0.44
alr 3841473 c.-53G>A upstream_gene_variant 0.72
embC 4241022 p.Ala387Val missense_variant 0.36
embC 4242075 p.Arg738Gln missense_variant 0.62
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.45
embA 4244350 p.Leu373Pro missense_variant 0.46
embB 4247847 p.Gln445Arg missense_variant 0.34
aftB 4267647 p.Asp397Gly missense_variant 0.31
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338624 c.-103C>A upstream_gene_variant 0.59
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.28
gid 4407927 p.Glu92Asp missense_variant 0.39