TB-Profiler result

Run: SRR25827513
Summary

Run ID: SRR25827513

Sample name:

Date: 02-02-2024 07:21:56

Number of reads: 9708260

Percentage reads mapped: 98.49

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 (0.68), rpoB p.Ile480Val (0.35), rpoB p.Ile491Phe (0.38)
Isoniazid R fabG1 c.-15C>T (0.19), katG p.Ser315Thr (1.00), katG p.Thr275Ala (0.22)
Ethambutol R embA c.-11C>A (0.18), embB p.Met306Val (0.67), embB p.Gln497Arg (0.30)
Pyrazinamide R pncA p.Leu27Pro (0.19)
Streptomycin R rpsL p.Lys43Arg (0.32), rrs n.514A>C (0.41), rrs n.906A>G (0.41)
Fluoroquinolones R gyrB p.Arg446Cys (0.34), gyrA p.Asp94Gly (0.67)
Moxifloxacin R gyrB p.Arg446Cys (0.34), gyrA p.Asp94Gly (0.67)
Ofloxacin R gyrB p.Arg446Cys (0.34), gyrA p.Asp94Gly (0.67)
Levofloxacin R gyrB p.Arg446Cys (0.34), gyrA p.Asp94Gly (0.67)
Ciprofloxacin R gyrB p.Arg446Cys (0.34), gyrA p.Asp94Gly (0.67)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.19)
Clofazimine
Para-aminosalicylic_acid
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 0.26
lineage2 East-Asian Beijing RD105 0.73
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.72
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.72
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 0.34 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.67 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.68 rifampicin
rpoB 761244 p.Ile480Val missense_variant 0.35 rifampicin
rpoB 761277 p.Ile491Phe missense_variant 0.38 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.32 streptomycin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.41 streptomycin
rrs 1472751 n.906A>G non_coding_transcript_exon_variant 0.41 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.19 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155289 p.Thr275Ala missense_variant 0.22 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 0.19 pyrazinamide
embA 4243222 c.-11C>A upstream_gene_variant 0.18 ethambutol
embB 4247429 p.Met306Val missense_variant 0.67 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.3 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 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.51
ccsA 620625 p.Ile245Met missense_variant 0.72
rpoB 759746 c.-61C>T upstream_gene_variant 0.27
rpoC 762434 c.-936T>G upstream_gene_variant 0.32
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 764817 p.Val483Gly missense_variant 0.28
rpoC 766488 p.Pro1040Arg missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.56
mmpR5 779130 c.144dupC frameshift_variant 0.35
mmpS5 779615 c.-710C>G upstream_gene_variant 0.73
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.7
embR 1416622 c.726C>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.73
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 0.33
pncA 2289240 c.2T>G start_lost 0.38
pncA 2289365 c.-125delC upstream_gene_variant 0.24
ahpC 2726105 c.-88G>A upstream_gene_variant 0.31
ribD 2987506 p.Leu223Arg missense_variant 0.16
Rv2752c 3067039 c.-848T>C upstream_gene_variant 0.31
thyX 3067949 c.-4C>T upstream_gene_variant 0.15
thyA 3073687 p.Ala262Val missense_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449326 p.Arg275Ser missense_variant 0.36
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568555 p.Leu42Pro missense_variant 0.21
Rv3236c 3612813 p.Thr102Ala missense_variant 0.75
alr 3841473 c.-53G>A upstream_gene_variant 0.3
embC 4242075 p.Arg738Gln missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.76
embA 4245835 p.Leu868Arg missense_variant 0.19
embB 4247015 p.Ser168Ala missense_variant 0.28
aftB 4267492 p.Ala449Thr missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 0.63
ethA 4326676 p.Ser266Arg missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.75
gid 4408114 p.Gly30Asp missense_variant 0.29