TB-Profiler result

Run: SRR25827403
Summary

Run ID: SRR25827403

Sample name:

Date: 21-03-2024 06:30:47

Number of reads: 8091432

Percentage reads mapped: 98.93

Strain: lineage3;lineage2.2.1.1

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 (0.47)
Isoniazid R katG p.Ser315Thr (0.46)
Ethambutol R embB p.Met306Val (0.20)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.32)
Fluoroquinolones R gyrA p.Asp94Gly (0.21)
Moxifloxacin R gyrA p.Asp94Gly (0.21)
Ofloxacin R gyrA p.Asp94Gly (0.21)
Levofloxacin R gyrA p.Asp94Gly (0.21)
Ciprofloxacin R gyrA p.Asp94Gly (0.21)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
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 0.61
lineage2 East-Asian Beijing RD105 0.33
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.35
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.33
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.13
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 7582 p.Asp94Gly missense_variant 0.21 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.47 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.32 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.46 isoniazid
embB 4247429 p.Met306Val missense_variant 0.2 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 7276 c.-26T>G upstream_gene_variant 0.59
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 0.96
mshA 575907 p.Ala187Val missense_variant 0.26
ccsA 620625 p.Ile245Met missense_variant 0.4
rpoB 759746 c.-61C>T upstream_gene_variant 0.64
rpoC 762434 c.-936T>G upstream_gene_variant 0.66
rpoC 763031 c.-339T>C upstream_gene_variant 0.97
rpoC 766641 p.His1091Arg missense_variant 0.56
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.94
mmpL5 776182 p.Asp767Asn missense_variant 0.26
mmpS5 779615 c.-710C>G upstream_gene_variant 0.32
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 0.98
rpsA 1834177 c.636A>C synonymous_variant 0.38
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.96
PPE35 2167926 p.Leu896Ser missense_variant 0.95
Rv1979c 2222685 p.Lys160Asn missense_variant 0.58
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.61
pncA 2289365 c.-125delC upstream_gene_variant 0.62
ahpC 2726105 c.-88G>A upstream_gene_variant 0.65
thyX 3067419 p.Pro176Leu missense_variant 0.59
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568857 c.-178C>T upstream_gene_variant 0.55
Rv3236c 3612813 p.Thr102Ala missense_variant 0.35
panD 4044023 c.259C>T synonymous_variant 0.53
embC 4242075 p.Arg738Gln missense_variant 0.6
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.35
aftB 4267647 p.Asp397Gly missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.97
gid 4407927 p.Glu92Asp missense_variant 0.3
gid 4408052 p.Asn51Asp missense_variant 0.57