TB-Profiler result

Run: SRR25827484

Summary

Run ID: SRR25827484

Sample name:

Date: 02-02-2024 05:16:08

Number of reads: 10591745

Percentage reads mapped: 98.92

Strain: lineage4;lineage3;lineage2.2.1;lineage1

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 (0.91)
Isoniazid R fabG1 c.-15C>T (0.16), katG p.Ser315Thr (0.90)
Ethambutol R embB p.Met306Val (0.49), embB p.Gln497Arg (0.17)
Pyrazinamide R pncA p.Gly132Ala (0.17), pncA p.Leu27Pro (0.29)
Streptomycin R rpsL p.Lys43Arg (0.72), gid p.Tyr22* (0.13)
Fluoroquinolones R gyrA p.Ala90Val (0.15), gyrA p.Asp94Gly (0.45)
Moxifloxacin R gyrA p.Ala90Val (0.15), gyrA p.Asp94Gly (0.45)
Ofloxacin R gyrA p.Ala90Val (0.15), gyrA p.Asp94Gly (0.45)
Levofloxacin R gyrA p.Ala90Val (0.15), gyrA p.Asp94Gly (0.45)
Ciprofloxacin R gyrA p.Ala90Val (0.15), gyrA p.Asp94Gly (0.45)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.16)
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 0.12
lineage2 East-Asian Beijing RD105 0.63
lineage4 Euro-American LAM;T;S;X;H None 0.06
lineage1 Indo-Oceanic EAI RD239 0.18
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.64
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.64
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 7570 p.Ala90Val missense_variant 0.15 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.45 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.91 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.72 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.16 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.9 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.17 pyrazinamide
pncA 2289162 p.Leu27Pro missense_variant 0.29 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.49 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.17 ethambutol
gid 4408137 p.Tyr22* stop_gained 0.13 streptomycin
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 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.95
gyrA 8452 p.Ala384Val missense_variant 0.16
gyrA 9143 c.1842T>C synonymous_variant 0.19
gyrA 9304 p.Gly668Asp missense_variant 0.9
fgd1 491290 p.Val170Met missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 0.92
mshA 575907 p.Ala187Val missense_variant 0.38
ccsA 620625 p.Ile245Met missense_variant 0.58
rpoC 762434 c.-936T>G upstream_gene_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 0.94
rpoC 763884 p.Ala172Val missense_variant 0.19
rpoC 763886 c.517C>A synonymous_variant 0.19
rpoC 764363 p.Gly332Ser missense_variant 0.15
rpoC 764840 p.Ile491Val missense_variant 0.21
rpoC 766488 p.Pro1040Arg missense_variant 0.24
rpoC 767181 p.Ala1271Val missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.92
mmpL5 776182 p.Asp767Asn missense_variant 0.33
mmpL5 776395 p.Phe696Leu missense_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 0.65
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.63
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
katG 2154724 p.Arg463Leu missense_variant 0.94
PPE35 2167926 p.Leu896Ser missense_variant 0.94
Rv1979c 2222308 p.Asp286Gly missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.16
ahpC 2726051 c.-142G>A upstream_gene_variant 0.15
folC 2747470 p.Ile43Ala missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 0.95
Rv3083 3448714 p.Asp71His missense_variant 0.15
Rv3083 3448936 p.Tyr145Asp missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.91
fprA 3475159 p.Asn385Asp missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 0.6
fbiA 3640457 c.-86G>C upstream_gene_variant 0.29
clpC1 4040517 p.Val63Ala missense_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 0.2
embC 4241022 p.Ala387Val missense_variant 0.17
embC 4241042 p.Asn394Asp missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.6
embA 4245969 p.Pro913Ser missense_variant 0.21
embB 4247028 p.Leu172Arg missense_variant 0.19
embB 4247646 p.Glu378Ala missense_variant 0.19
aftB 4267647 p.Asp397Gly missense_variant 0.6
ubiA 4269387 p.Glu149Asp missense_variant 0.2
aftB 4269606 c.-770T>C upstream_gene_variant 0.17
ethA 4326069 p.Arg469Trp missense_variant 0.32
ethA 4326676 p.Ser266Arg missense_variant 0.27
ethA 4326878 p.Ala199Asp missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.18
gid 4407588 c.615A>G synonymous_variant 0.93
gid 4407620 p.Tyr195His missense_variant 0.24
gid 4407873 c.330G>T synonymous_variant 0.17
gid 4407927 p.Glu92Asp missense_variant 0.6