TB-Profiler result

Run: SRR25827427

Summary

Run ID: SRR25827427

Sample name:

Date: 02-02-2024 02:47:51

Number of reads: 4822364

Percentage reads mapped: 98.93

Strain: lineage4;lineage3;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 (0.80)
Isoniazid R fabG1 c.-15C>T (0.21), katG p.Ser315Thr (0.76)
Ethambutol R embB p.Met306Val (0.16), embB p.Gln497Arg (0.19)
Pyrazinamide R pncA p.Gly132Ala (0.19), pncA p.Asp63Gly (0.14)
Streptomycin R rpsL p.Lys43Arg (0.35)
Fluoroquinolones R gyrA p.Gly88Ala (0.13)
Moxifloxacin R gyrA p.Gly88Ala (0.13)
Ofloxacin R gyrA p.Gly88Ala (0.13)
Levofloxacin R gyrA p.Gly88Ala (0.13)
Ciprofloxacin R gyrA p.Gly88Ala (0.13)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.21)
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 0.28
lineage2 East-Asian Beijing RD105 0.25
lineage4 Euro-American LAM;T;S;X;H None 0.08
lineage1 Indo-Oceanic EAI RD239 0.37
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.24
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.34
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.24
lineage1.2.2.2 Indo-Oceanic NA RD239 0.34
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 7564 p.Gly88Ala missense_variant 0.13 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.8 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.35 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.21 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.76 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.19 pyrazinamide
pncA 2289054 p.Asp63Gly missense_variant 0.14 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.16 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.19 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 5052 c.-188A>G upstream_gene_variant 0.2
gyrB 5075 c.-165C>T upstream_gene_variant 0.35
gyrB 5201 c.-39A>G upstream_gene_variant 0.38
gyrB 6112 p.Met291Ile missense_variant 0.34
gyrB 7158 c.1931_1933delCCG disruptive_inframe_deletion 0.37
gyrA 7268 c.-34C>T upstream_gene_variant 0.32
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.91
gyrA 8452 p.Ala384Val missense_variant 0.34
gyrA 9143 c.1842T>C synonymous_variant 0.36
gyrA 9304 p.Gly668Asp missense_variant 0.96
fgd1 491290 p.Val170Met missense_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 0.94
mshA 575907 p.Ala187Val missense_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 0.19
rpoB 759746 c.-61C>T upstream_gene_variant 0.28
rpoC 762434 c.-936T>G upstream_gene_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 0.89
rpoC 763884 p.Ala172Val missense_variant 0.46
rpoC 763886 c.517C>A synonymous_variant 0.45
rpoC 764840 p.Ile491Val missense_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.93
mmpL5 776182 p.Asp767Asn missense_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781879 p.Val107Ala missense_variant 0.22
Rv1258c 1406170 p.Gly391Arg missense_variant 0.44
Rv1258c 1406760 c.580_581insC frameshift_variant 0.23
embR 1417019 p.Cys110Tyr missense_variant 0.35
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471754 n.-92T>G upstream_gene_variant 0.38
rpsA 1834177 c.636A>C synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101756 c.1287G>T synonymous_variant 0.41
katG 2154724 p.Arg463Leu missense_variant 0.9
PPE35 2167926 p.Leu896Ser missense_variant 0.93
PPE35 2168742 p.Gly624Asp missense_variant 0.37
Rv1979c 2222308 p.Asp286Gly missense_variant 0.45
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.23
pncA 2289365 c.-125delC upstream_gene_variant 0.29
kasA 2518132 c.18C>T synonymous_variant 0.34
eis 2714177 p.Leu386Ile missense_variant 0.31
ahpC 2726051 c.-142G>A upstream_gene_variant 0.49
ahpC 2726105 c.-88G>A upstream_gene_variant 0.28
ald 3086788 c.-32T>C upstream_gene_variant 0.95
Rv3083 3448714 p.Asp71His missense_variant 0.41
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.9
fprA 3474597 c.591C>A synonymous_variant 0.37
fprA 3475159 p.Asn385Asp missense_variant 0.31
Rv3236c 3612563 p.Met185Thr missense_variant 0.24
Rv3236c 3612813 p.Thr102Ala missense_variant 0.2
clpC1 4040517 p.Val63Ala missense_variant 0.39
embC 4240671 p.Thr270Ile missense_variant 0.37
embC 4241022 p.Ala387Val missense_variant 0.17
embC 4241042 p.Asn394Asp missense_variant 0.37
embC 4242075 p.Arg738Gln missense_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.15
embA 4245969 p.Pro913Ser missense_variant 0.41
embB 4247028 p.Leu172Arg missense_variant 0.26
embB 4247646 p.Glu378Ala missense_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 0.27
ubiA 4269387 p.Glu149Asp missense_variant 0.41
aftB 4269606 c.-770T>C upstream_gene_variant 0.44
ethA 4326148 c.1326G>T synonymous_variant 0.31
ethA 4326439 p.Asn345Lys missense_variant 0.29
whiB6 4338203 p.Arg107Cys missense_variant 0.33
whiB6 4338533 c.-12T>C upstream_gene_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.46
gid 4407588 c.615A>G synonymous_variant 0.93
gid 4407620 p.Tyr195His missense_variant 0.18
gid 4407873 c.330G>T synonymous_variant 0.41
gid 4407927 p.Glu92Asp missense_variant 0.2