TB-Profiler result

Run: SRR25827776
Summary

Run ID: SRR25827776

Sample name:

Date: 16-03-2024 07:19:28

Number of reads: 3761989

Percentage reads mapped: 50.45

Strain: lineage4.3.4.2;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 (0.59)
Isoniazid R katG p.Ser315Thr (0.35)
Ethambutol R embB p.Gly406Asp (0.41), embB p.Gln853Pro (0.39)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.42)
Fluoroquinolones R gyrA p.Ala90Val (0.49)
Moxifloxacin R gyrA p.Ala90Val (0.49)
Ofloxacin R gyrA p.Ala90Val (0.49)
Levofloxacin R gyrA p.Ala90Val (0.49)
Ciprofloxacin R gyrA p.Ala90Val (0.49)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.50)
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 0.4
lineage4 Euro-American LAM;T;S;X;H None 0.59
lineage4.3 Euro-American (LAM) mainly-LAM None 0.57
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.4
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.44
lineage4.3.4 Euro-American (LAM) LAM RD174 0.61
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.57
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 0.49 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.59 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.42 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.35 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 0.5 para-aminosalicylic_acid
embB 4247730 p.Gly406Asp missense_variant 0.41 ethambutol
embB 4249071 p.Gln853Pro missense_variant 0.39 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 6140 p.Val301Leu missense_variant 0.58
gyrA 7283 c.-19G>T upstream_gene_variant 0.47
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 0.37
mshA 575907 p.Ala187Val missense_variant 0.45
ccsA 620625 p.Ile245Met missense_variant 0.33
rpoB 761942 c.2136C>T synonymous_variant 0.6
rpoC 763031 c.-339T>C upstream_gene_variant 0.36
rpoC 764995 c.1626C>G synonymous_variant 0.59
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.37
mmpL5 776182 p.Asp767Asn missense_variant 0.37
mmpS5 779615 c.-710C>G upstream_gene_variant 0.39
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.46
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.39
PPE35 2167926 p.Leu896Ser missense_variant 0.41
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.52
thyA 3074069 p.Val135Phe missense_variant 0.45
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.34
whiB7 3568428 c.252A>C synonymous_variant 0.26
Rv3236c 3612009 p.Ala370Thr missense_variant 0.65
Rv3236c 3612813 p.Thr102Ala missense_variant 0.32
alr 3840719 c.702A>G synonymous_variant 0.6
clpC1 4038287 c.2418C>T synonymous_variant 0.61
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.48
embB 4249757 p.Thr1082Ala missense_variant 0.38
aftB 4267647 p.Asp397Gly missense_variant 0.36
ethA 4327060 p.Ser138Arg missense_variant 0.38
whiB6 4338325 p.Ala66Asp missense_variant 0.44
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.53
gid 4407927 p.Glu92Asp missense_variant 0.44
gid 4408156 p.Leu16Arg missense_variant 0.59