TB-Profiler result

Run: SRR25827461
Summary

Run ID: SRR25827461

Sample name:

Date: 15-03-2024 14:23:20

Number of reads: 9260106

Percentage reads mapped: 98.91

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 (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.54), embB p.Gly406Ala (0.32), embB p.Asp1024Asn (0.21)
Pyrazinamide R pncA p.Thr160Ala (0.24), pncA c.390_391dupGG (0.27), pncA c.390_391dupGG (0.27), pncA p.Leu27Pro (0.44)
Streptomycin R rpsL p.Lys43Arg (0.46), rpsL p.Lys88Arg (0.21), gid c.115delC (0.26)
Fluoroquinolones R gyrA p.Asp94Gly (0.56)
Moxifloxacin R gyrA p.Asp94Gly (0.56)
Ofloxacin R gyrA p.Asp94Gly (0.56)
Levofloxacin R gyrA p.Asp94Gly (0.56)
Ciprofloxacin R gyrA p.Asp94Gly (0.56)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.10_19dupCACCTCGACG (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 0.53
lineage2 East-Asian Beijing RD105 0.46
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.47
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.46
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 0.56 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.46 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.21 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288764 p.Thr160Ala missense_variant 0.24 pyrazinamide
pncA 2288850 c.390_391dupGG frameshift_variant 0.27 pyrazinamide, pyrazinamide
pncA 2289162 p.Leu27Pro missense_variant 0.44 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.54 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.32 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.21 ethambutol
ethA 4327454 c.10_19dupCACCTCGACG frameshift_variant 0.21 ethionamide
gid 4408087 c.115delC frameshift_variant 0.26 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
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
ccsA 620625 p.Ile245Met missense_variant 0.49
rpoB 759746 c.-61C>T upstream_gene_variant 0.54
rpoC 762434 c.-936T>G upstream_gene_variant 0.52
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766488 p.Pro1040Arg missense_variant 0.4
rpoC 767123 p.Val1252Leu missense_variant 0.19
rpoC 767181 p.Ala1271Val missense_variant 0.46
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.51
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.47
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.48
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 2168761 p.Pro618Thr missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.31
pncA 2289365 c.-125delC upstream_gene_variant 0.55
ahpC 2726105 c.-88G>A upstream_gene_variant 0.54
folC 2747470 p.Ile43Ala missense_variant 0.27
Rv2752c 3065297 p.Gln299* stop_gained 0.23
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448693 p.Tyr64Asp missense_variant 0.35
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.4
fbiA 3640346 c.-196delA upstream_gene_variant 0.3
fbiA 3640457 c.-86G>C upstream_gene_variant 0.55
fbiB 3642877 p.Lys448Arg missense_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 0.49
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.54
embA 4245014 c.1782C>G synonymous_variant 0.3
aftB 4267647 p.Asp397Gly missense_variant 0.41
ethA 4326069 p.Arg469Trp missense_variant 0.4
ethA 4326676 p.Ser266Arg missense_variant 0.51
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.44
gid 4408064 p.Arg47Gly missense_variant 0.28