TB-Profiler result

Run: SRR25827440
Summary

Run ID: SRR25827440

Sample name:

Date: 02-02-2024 03:42:07

Number of reads: 10926967

Percentage reads mapped: 98.72

Strain: lineage3;lineage2.2.1

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.Ser450Leu (0.56)
Isoniazid R katG p.Ser315Thr (0.45)
Ethambutol R embB p.Met306Val (0.52)
Pyrazinamide R pncA p.Tyr41* (0.47)
Streptomycin R rpsL p.Lys43Arg (0.44), gid c.102delG (0.57)
Fluoroquinolones R gyrA p.Ala90Val (0.44)
Moxifloxacin R gyrA p.Ala90Val (0.44)
Ofloxacin R gyrA p.Ala90Val (0.44)
Levofloxacin R gyrA p.Ala90Val (0.44)
Ciprofloxacin R gyrA p.Ala90Val (0.44)
Aminoglycosides R rrs n.1401A>G (0.40)
Amikacin R rrs n.1401A>G (0.40)
Capreomycin R rrs n.1401A>G (0.40)
Kanamycin R rrs n.1401A>G (0.40)
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.49)
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 0.47
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.49
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 7570 p.Ala90Val missense_variant 0.44 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.56 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.44 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.49 linezolid
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.4 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.45 isoniazid
pncA 2289119 p.Tyr41* stop_gained 0.47 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.52 ethambutol
gid 4408100 c.102delG frameshift_variant 0.57 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
gyrB 6737 p.Thr500Ala missense_variant 0.42
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8131 p.Gln277Arg missense_variant 0.51
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.49
ccsA 620553 c.663T>C synonymous_variant 0.51
ccsA 620625 p.Ile245Met missense_variant 0.49
rpoB 759746 c.-61C>T upstream_gene_variant 0.59
rpoC 762434 c.-936T>G upstream_gene_variant 0.5
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Ala missense_variant 0.52
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.47
mmpR5 779371 c.386delC frameshift_variant 0.44
mmpS5 779615 c.-710C>G upstream_gene_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.46
atpE 1461231 p.Ala63Pro missense_variant 0.49
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.44
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156344 c.-233C>G upstream_gene_variant 0.51
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.51
pncA 2289365 c.-125delC upstream_gene_variant 0.51
ahpC 2726105 c.-88G>A upstream_gene_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087626 c.808delG frameshift_variant 0.49
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474773 p.Ala256Gly missense_variant 0.45
whiB7 3568425 c.255T>G synonymous_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 0.51
clpC1 4040753 c.-49G>A upstream_gene_variant 0.58
embC 4242075 p.Arg738Gln missense_variant 0.51
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.47
embB 4247028 p.Leu172Arg missense_variant 0.19
embB 4249757 p.Thr1082Ala missense_variant 0.47
aftB 4267647 p.Asp397Gly missense_variant 0.37
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.56