TB-Profiler result

Run: SRR25827868

Summary

Run ID: SRR25827868

Sample name:

Date: 02-02-2024 23:37:36

Number of reads: 19003630

Percentage reads mapped: 99.49

Strain: lineage3.1.2;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 (0.33)
Isoniazid R katG p.Ser315Thr (0.37)
Ethambutol R embB p.Met306Val (0.34), embB p.Gln853Pro (0.35)
Pyrazinamide R pncA p.Val139Ala (0.35)
Streptomycin R rpsL p.Lys43Arg (0.37)
Fluoroquinolones R gyrA p.Ala90Val (0.64), gyrA p.Asp94Gly (0.37)
Moxifloxacin R gyrA p.Ala90Val (0.64), gyrA p.Asp94Gly (0.37)
Ofloxacin R gyrA p.Ala90Val (0.64), gyrA p.Asp94Gly (0.37)
Levofloxacin R gyrA p.Ala90Val (0.64), gyrA p.Asp94Gly (0.37)
Ciprofloxacin R gyrA p.Ala90Val (0.64), gyrA p.Asp94Gly (0.37)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.1047dupT (0.33), ethA c.1047dupT (0.33)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.36)
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 0.65
lineage2 East-Asian Beijing RD105 0.35
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.34
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.63
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.62
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.36
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 0.64 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.37 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.33 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.37 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.37 isoniazid
pncA 2288826 p.Val139Ala missense_variant 0.35 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.36 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.34 ethambutol
embB 4249071 p.Gln853Pro missense_variant 0.35 ethambutol
ethA 4326426 c.1047dupT frameshift_variant 0.33 ethionamide, ethionamide
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 7283 c.-19G>T upstream_gene_variant 0.36
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
mshA 575907 p.Ala187Val missense_variant 0.34
ccsA 620625 p.Ile245Met missense_variant 0.34
rpoB 759746 c.-61C>T upstream_gene_variant 0.62
rpoC 762434 c.-936T>G upstream_gene_variant 0.62
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764666 p.Gly433Ser missense_variant 0.34
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.37
mmpS5 779615 c.-710C>G upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.34
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 0.67
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 0.65
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.6
pncA 2289365 c.-125delC upstream_gene_variant 0.63
ahpC 2726105 c.-88G>A upstream_gene_variant 0.62
pepQ 2860365 c.54G>T synonymous_variant 0.37
thyA 3074069 p.Val135Phe missense_variant 0.36
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086931 p.Gly38Ser missense_variant 0.66
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.34
embC 4239852 c.-11G>A upstream_gene_variant 0.63
embC 4242075 p.Arg738Gln missense_variant 0.66
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 0.38
embA 4243460 c.228C>T synonymous_variant 0.38
embB 4247028 p.Leu172Arg missense_variant 0.18
embB 4247039 p.Phe176Val missense_variant 0.13
embB 4249757 p.Thr1082Ala missense_variant 0.38
aftB 4267647 p.Asp397Gly missense_variant 0.4
ethA 4326911 p.Val188Gly missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.38