TB-Profiler result

Run: SRR25827489

Summary

Run ID: SRR25827489

Sample name:

Date: 02-02-2024 05:29:30

Number of reads: 8079688

Percentage reads mapped: 95.89

Strain: lineage3.1.2.1;lineage2.2.1;lineage1.1.2

Drug-resistance: 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 (0.83)
Isoniazid R katG p.Ser315Thr (0.84)
Ethambutol R embB p.Met306Val (0.23)
Pyrazinamide R pncA p.Leu159Arg (0.25), pncA p.Asp12Ala (0.64)
Streptomycin R rpsL p.Lys43Arg (0.79)
Fluoroquinolones R gyrA p.Asp94Gly (0.58)
Moxifloxacin R gyrA p.Asp94Gly (0.58)
Ofloxacin R gyrA p.Asp94Gly (0.58)
Levofloxacin R gyrA p.Asp94Gly (0.58)
Ciprofloxacin R gyrA p.Asp94Gly (0.58)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine R mmpR5 c.198dupG (0.18)
Para-aminosalicylic_acid
Delamanid
Bedaquiline R mmpR5 c.198dupG (0.18)
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.58
lineage2 East-Asian Beijing RD105 0.25
lineage1 Indo-Oceanic EAI RD239 0.15
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.18
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.23
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.59
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.15
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.58
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.24
lineage3.1.2.1 East-African-Indian CAS2 RD750 0.6
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.Asp94Gly missense_variant 0.58 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.83 rifampicin
mmpR5 779181 c.198dupG frameshift_variant 0.18 clofazimine, bedaquiline
rpsL 781687 p.Lys43Arg missense_variant 0.79 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.84 isoniazid
pncA 2288766 p.Leu159Arg missense_variant 0.25 pyrazinamide
pncA 2289207 p.Asp12Ala missense_variant 0.64 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.23 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 6112 p.Met291Ile missense_variant 0.19
gyrB 6124 c.885C>T synonymous_variant 0.19
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.38
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.23
ccsA 619968 c.78G>A synonymous_variant 0.62
ccsA 620625 p.Ile245Met missense_variant 0.25
rpoB 759746 c.-61C>T upstream_gene_variant 0.69
rpoC 762434 c.-936T>G upstream_gene_variant 0.59
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.18
rpoC 763886 c.517C>A synonymous_variant 0.18
rpoC 764916 p.Leu516Pro missense_variant 0.52
rpoC 765171 p.Pro601Leu missense_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.29
mmpL5 776395 p.Phe696Leu missense_variant 0.15
mmpS5 778883 p.Ala8Val missense_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 0.24
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303953 c.1023C>T synonymous_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 0.18
Rv1258c 1406878 p.Ile155Val missense_variant 0.21
embR 1417236 p.Val38Met missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.29
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
PPE35 2168604 p.Pro670Leu missense_variant 0.55
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.52
pncA 2289365 c.-125delC upstream_gene_variant 0.57
ahpC 2726051 c.-142G>A upstream_gene_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 0.59
Rv2752c 3064632 c.1560C>T synonymous_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448554 c.51C>T synonymous_variant 0.58
Rv3083 3448714 p.Asp71His missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 0.29
rpoA 3878416 p.Gly31Ala missense_variant 0.27
clpC1 4040517 p.Val63Ala missense_variant 0.16
embC 4240671 p.Thr270Ile missense_variant 0.24
embC 4241022 p.Ala387Val missense_variant 0.24
embC 4241042 p.Asn394Asp missense_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 0.57
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243192 c.-40delT upstream_gene_variant 0.63
embA 4243460 c.228C>T synonymous_variant 0.27
embA 4243848 p.Val206Met missense_variant 0.18
embA 4244515 p.Ala428Val missense_variant 0.59
embB 4247646 p.Glu378Ala missense_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.21
gid 4407927 p.Glu92Asp missense_variant 0.26