TB-Profiler result

Run: SRR25827293

Summary

Run ID: SRR25827293

Sample name:

Date: 31-01-2024 18:11:12

Number of reads: 27596199

Percentage reads mapped: 98.47

Strain: lineage2.2.1;lineage1.2.2.2

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 (0.78)
Isoniazid R fabG1 c.-15C>T (0.72), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Asp354Ala (0.20), embB p.Gln497Arg (0.56)
Pyrazinamide R pncA p.Gly132Ala (0.70)
Streptomycin R rpsL p.Lys43Arg (0.81), rrs n.517C>T (0.38)
Fluoroquinolones R gyrA p.Asp94Ala (0.75)
Moxifloxacin R gyrA p.Asp94Ala (0.75)
Ofloxacin R gyrA p.Asp94Ala (0.75)
Levofloxacin R gyrA p.Asp94Ala (0.75)
Ciprofloxacin R gyrA p.Asp94Ala (0.75)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.72)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.7
lineage1 Indo-Oceanic EAI RD239 0.3
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.73
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.28
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.68
lineage1.2.2.2 Indo-Oceanic NA RD239 0.26
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 7582 p.Asp94Ala missense_variant 0.75 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.78 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.81 streptomycin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.38 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.72 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.7 pyrazinamide
embB 4247574 p.Asp354Ala missense_variant 0.2 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.56 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
gyrB 5075 c.-165C>T upstream_gene_variant 0.29
gyrB 6112 p.Met291Ile missense_variant 0.23
gyrA 7268 c.-34C>T upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.14
gyrA 9143 c.1842T>C synonymous_variant 0.19
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490977 c.195C>G synonymous_variant 0.31
fgd1 491290 p.Val170Met missense_variant 0.68
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.8
ccsA 620625 p.Ile245Met missense_variant 0.59
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.29
rpoC 763886 c.517C>A synonymous_variant 0.3
rpoC 764840 p.Ile491Val missense_variant 0.64
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.66
mmpS5 779615 c.-710C>G upstream_gene_variant 0.75
mmpS5 779625 c.-720G>A upstream_gene_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.67
embR 1417019 p.Cys110Tyr missense_variant 0.42
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.62
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 0.31
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.33
Rv1979c 2222308 p.Asp286Gly missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 0.27
Rv2752c 3064700 p.Ser498Pro missense_variant 0.58
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.21
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.15
fprA 3475159 p.Asn385Asp missense_variant 0.27
Rv3236c 3612813 p.Thr102Ala missense_variant 0.75
clpC1 4040517 p.Val63Ala missense_variant 0.36
clpC1 4040719 c.-15A>G upstream_gene_variant 0.41
embC 4240671 p.Thr270Ile missense_variant 0.33
embC 4241022 p.Ala387Val missense_variant 0.69
embC 4241042 p.Asn394Asp missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.64
embA 4245969 p.Pro913Ser missense_variant 0.27
embB 4246544 p.Thr11Pro missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.25
embB 4246555 c.42G>C synonymous_variant 0.19
embB 4247646 p.Glu378Ala missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 0.69
aftB 4267960 p.Val293Met missense_variant 0.24
ubiA 4269387 p.Glu149Asp missense_variant 0.15
aftB 4269606 c.-770T>C upstream_gene_variant 0.26
ethA 4326148 c.1326G>T synonymous_variant 0.24
ethA 4326439 p.Asn345Lys missense_variant 0.23
whiB6 4338203 p.Arg107Cys missense_variant 0.31
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.24
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.72
gid 4407848 p.Ala119Thr missense_variant 0.3
gid 4407873 c.330G>T synonymous_variant 0.27
gid 4407927 p.Glu92Asp missense_variant 0.67