TB-Profiler result

Run: SRR25827527

Summary

Run ID: SRR25827527

Sample name:

Date: 02-02-2024 08:38:55

Number of reads: 9053789

Percentage reads mapped: 99.11

Strain: lineage4.2.2.2;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.His445Gly (0.70), rpoB p.Ser450Leu (0.30)
Isoniazid R fabG1 c.-15C>T (0.23), katG p.Ser315Thr (0.28)
Ethambutol R embB p.Gln497Arg (0.30)
Pyrazinamide R pncA p.Gly132Ala (0.27)
Streptomycin R rpsL p.Lys43Arg (0.23)
Fluoroquinolones R gyrA p.Ala90Val (0.68), gyrA p.Asp94Gly (0.28)
Moxifloxacin R gyrA p.Ala90Val (0.68), gyrA p.Asp94Gly (0.28)
Ofloxacin R gyrA p.Ala90Val (0.68), gyrA p.Asp94Gly (0.28)
Levofloxacin R gyrA p.Ala90Val (0.68), gyrA p.Asp94Gly (0.28)
Ciprofloxacin R gyrA p.Ala90Val (0.68), gyrA p.Asp94Gly (0.28)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.23)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.27
lineage4 Euro-American LAM;T;S;X;H None 0.71
lineage4.2 Euro-American H;T;LAM None 0.74
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.27
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.7
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.27
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.71
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 0.68 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.28 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Gly missense_variant 0.7 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.3 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.23 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.23 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.28 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.27 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.3 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 0.69
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 0.27
mshA 575907 p.Ala187Val missense_variant 0.25
mshA 576077 c.730C>T synonymous_variant 0.7
ccsA 620625 p.Ile245Met missense_variant 0.25
rpoB 761489 c.1683G>A synonymous_variant 0.71
rpoC 763031 c.-339T>C upstream_gene_variant 0.26
rpoC 764840 p.Ile491Val missense_variant 0.26
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.31
mmpL5 776182 p.Asp767Asn missense_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.27
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.3
PPE35 2167926 p.Leu896Ser missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289433 c.-192C>T upstream_gene_variant 0.68
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.7
ald 3086742 c.-78A>C upstream_gene_variant 0.76
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.26
embC 4241022 p.Ala387Val missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243201 c.-31delC upstream_gene_variant 0.69
embA 4243460 c.228C>T synonymous_variant 0.32
embB 4247028 p.Leu172Arg missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 0.32
ethA 4327905 c.-432C>T upstream_gene_variant 0.78
whiB6 4338260 p.Arg88Trp missense_variant 0.73
whiB6 4338333 c.188dupC frameshift_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.29
gid 4407620 p.Tyr195His missense_variant 0.29
gid 4407927 p.Glu92Asp missense_variant 0.23