TB-Profiler result

Run: SRR25827444
Summary

Run ID: SRR25827444

Sample name:

Date: 15-03-2024 13:38:42

Number of reads: 7607437

Percentage reads mapped: 98.91

Strain: lineage3

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 (1.00), rpoC p.Leu527Val (0.97)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.99)
Pyrazinamide
Streptomycin R rpsL p.Lys88Thr (0.99), gid c.102delG (0.98)
Fluoroquinolones R gyrA p.Asp94Asn (0.95)
Moxifloxacin R gyrA p.Asp94Asn (0.95)
Ofloxacin R gyrA p.Asp94Asn (0.95)
Levofloxacin R gyrA p.Asp94Asn (0.95)
Ciprofloxacin R gyrA p.Asp94Asn (0.95)
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 0.96
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 7581 p.Asp94Asn missense_variant 0.95 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764948 p.Leu527Val missense_variant 0.97 rifampicin
rpsL 781822 p.Lys88Thr missense_variant 0.99 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 0.99 ethambutol
gid 4408100 c.102delG frameshift_variant 0.98 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 1.0
mshA 575283 c.-65C>G upstream_gene_variant 0.96
mshA 575655 c.310dupG frameshift_variant 0.97
mshA 576453 p.Val369Gly missense_variant 0.25
rpoB 759746 c.-61C>T upstream_gene_variant 0.98
rpoC 762434 c.-936T>G upstream_gene_variant 0.97
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 779130 c.144dupC frameshift_variant 0.93
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416814 c.534G>A synonymous_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167964 c.2648dupC frameshift_variant 0.94
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.96
pncA 2289239 c.3G>A start_lost 0.93
pncA 2289365 c.-125delC upstream_gene_variant 0.97
ahpC 2726105 c.-88G>A upstream_gene_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086953 c.135dupC frameshift_variant 0.85
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568857 c.-178C>T upstream_gene_variant 0.96
fbiA 3640421 c.-122C>A upstream_gene_variant 0.97
panD 4044023 c.259C>T synonymous_variant 0.98
embC 4242075 p.Arg738Gln missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245835 p.Leu868Arg missense_variant 0.17
embB 4247028 p.Leu172Arg missense_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0