TB-Profiler result

Run: SRR25827643

Summary

Run ID: SRR25827643

Sample name:

Date: 02-02-2024 13:21:36

Number of reads: 9372515

Percentage reads mapped: 99.0

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.Ser450Leu (1.00), rpoC p.Ile491Thr (0.19)
Isoniazid R fabG1 c.-15C>T (0.34), katG p.Ser315Thr (1.00), katG p.Thr275Ala (0.27)
Ethambutol R embA c.-16C>T (0.14), embA c.-11C>A (0.22), embB p.Met306Val (0.47), embB p.Gln497Arg (0.40)
Pyrazinamide R pncA p.Leu27Pro (0.36), pncA p.Ile5Ser (0.13)
Streptomycin R rpsL p.Lys43Arg (0.75)
Fluoroquinolones R gyrB p.Arg446Cys (0.26), gyrA p.Ala90Val (0.16), gyrA p.Asp94Gly (0.59)
Moxifloxacin R gyrB p.Arg446Cys (0.26), gyrA p.Ala90Val (0.16), gyrA p.Asp94Gly (0.59)
Ofloxacin R gyrB p.Arg446Cys (0.26), gyrA p.Ala90Val (0.16), gyrA p.Asp94Gly (0.59)
Levofloxacin R gyrB p.Arg446Cys (0.26), gyrA p.Ala90Val (0.16), gyrA p.Asp94Gly (0.59)
Ciprofloxacin R gyrB p.Arg446Cys (0.26), gyrA p.Ala90Val (0.16), gyrA p.Asp94Gly (0.59)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.34)
Clofazimine
Para-aminosalicylic_acid R thyA p.Thr22Ala (0.17)
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 0.25
lineage2 East-Asian Beijing RD105 0.72
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.72
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.73
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
gyrB 6575 p.Arg446Cys missense_variant 0.26 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 0.16 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.59 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.19 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.75 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.34 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155289 p.Thr275Ala missense_variant 0.27 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 0.36 pyrazinamide
pncA 2289228 p.Ile5Ser missense_variant 0.13 pyrazinamide
thyA 3074408 p.Thr22Ala missense_variant 0.17 para-aminosalicylic_acid
embA 4243217 c.-16C>T upstream_gene_variant 0.14 ethambutol
embA 4243222 c.-11C>A upstream_gene_variant 0.22 ethambutol
embB 4247429 p.Met306Val missense_variant 0.47 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.4 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 0.3
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.37
ccsA 620625 p.Ile245Met missense_variant 0.71
rpoB 759746 c.-61C>T upstream_gene_variant 0.34
rpoC 762434 c.-936T>G upstream_gene_variant 0.23
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 0.3
rpoC 766488 p.Pro1040Arg missense_variant 0.35
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.35
mmpS5 779615 c.-710C>G upstream_gene_variant 0.75
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.73
embR 1416622 c.726C>T synonymous_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.76
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 2289047 c.195C>T synonymous_variant 0.28
pncA 2289365 c.-125delC upstream_gene_variant 0.27
ahpC 2726105 c.-88G>A upstream_gene_variant 0.36
thyX 3067949 c.-4C>T upstream_gene_variant 0.19
thyA 3073687 p.Ala262Val missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568555 p.Leu42Pro missense_variant 0.25
whiB7 3568854 c.-176delG upstream_gene_variant 0.24
Rv3236c 3612813 p.Thr102Ala missense_variant 0.69
alr 3841473 c.-53G>A upstream_gene_variant 0.24
embC 4241022 p.Ala387Val missense_variant 0.25
embC 4242075 p.Arg738Gln missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.73
embA 4245835 p.Leu868Arg missense_variant 0.2
embB 4247015 p.Ser168Ala missense_variant 0.27
aftB 4267492 p.Ala449Thr missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 0.68
ubiA 4269299 p.Ile179Leu missense_variant 0.14
ethA 4326676 p.Ser266Arg missense_variant 0.37
whiB6 4338292 p.Ala77Val missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.31
gid 4407927 p.Glu92Asp missense_variant 0.74
gid 4408114 p.Gly30Asp missense_variant 0.23