TB-Profiler result

Run: SRR25827439
Summary

Run ID: SRR25827439

Sample name:

Date: 21-03-2024 07:46:58

Number of reads: 5160101

Percentage reads mapped: 98.01

Strain: lineage3.1.2.1;lineage2.2.1.2

Drug-resistance: 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.Leu430Pro (0.23), rpoB p.Ser450Leu (0.73), rpoC p.Leu527Val (0.51)
Isoniazid R fabG1 c.-8T>C (0.35), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (0.41), embB p.Met306Ile (0.41)
Pyrazinamide R pncA p.Ala171Val (0.42)
Streptomycin R rpsL p.Lys43Arg (0.53), gid c.87delC (0.20)
Fluoroquinolones R gyrA p.Ala90Val (0.19), gyrA p.Asp94Ala (0.56)
Moxifloxacin R gyrA p.Ala90Val (0.19), gyrA p.Asp94Ala (0.56)
Ofloxacin R gyrA p.Ala90Val (0.19), gyrA p.Asp94Ala (0.56)
Levofloxacin R gyrA p.Ala90Val (0.19), gyrA p.Asp94Ala (0.56)
Ciprofloxacin R gyrA p.Ala90Val (0.19), gyrA p.Asp94Ala (0.56)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-8T>C (0.35), ethA p.Tyr408* (0.20)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rrl n.2814G>T (0.19)
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 0.38
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.34
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.3
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.41
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.33
lineage2.2.1.2 East-Asian (Beijing) Beijing-RD142 RD105;RD207;RD181;RD142 0.34
lineage3.1.2.1 East-African-Indian CAS2 RD750 0.34
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 0.19 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.56 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Pro missense_variant 0.23 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.73 rifampicin
rpoC 764948 p.Leu527Val missense_variant 0.51 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.53 streptomycin
rrl 1476471 n.2814G>T non_coding_transcript_exon_variant 0.19 linezolid
fabG1 1673432 c.-8T>C upstream_gene_variant 0.35 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288730 p.Ala171Val missense_variant 0.42 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.41 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.41 ethambutol
ethA 4326250 p.Tyr408* stop_gained 0.2 ethionamide
gid 4408115 c.87delC frameshift_variant 0.2 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 0.99
mshA 575907 p.Ala187Val missense_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 0.41
rpoB 759746 c.-61C>T upstream_gene_variant 0.64
rpoC 762434 c.-936T>G upstream_gene_variant 0.61
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764822 p.Asp485Tyr missense_variant 0.38
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.97
mmpL5 776182 p.Asp767Asn missense_variant 0.31
mmpS5 779615 c.-710C>G upstream_gene_variant 0.37
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.38
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 0.99
PPE35 2167926 p.Leu896Ser missense_variant 0.99
PPE35 2168604 p.Pro670Leu missense_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.57
pncA 2289365 c.-125delC upstream_gene_variant 0.65
ahpC 2726105 c.-88G>A upstream_gene_variant 0.66
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087862 p.Gly348Glu missense_variant 0.28
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.37
embC 4242075 p.Arg738Gln missense_variant 0.65
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.33
embA 4245131 c.1899G>A synonymous_variant 0.28
aftB 4267647 p.Asp397Gly missense_variant 0.29
ethA 4327415 p.Ala20Val missense_variant 0.3
whiB6 4338194 p.Arg110Trp missense_variant 0.33
whiB6 4338242 p.Gln94* stop_gained 0.35
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407742 p.Arg154Pro missense_variant 0.37
gid 4407927 p.Glu92Asp missense_variant 0.29