TB-Profiler result

Run: SRR25827472
Summary

Run ID: SRR25827472

Sample name:

Date: 21-03-2024 09:20:13

Number of reads: 6222270

Percentage reads mapped: 99.14

Strain: lineage3;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 (0.31)
Isoniazid R katG p.Ser315Thr (0.34)
Ethambutol R embB p.Gly406Ser (0.19)
Pyrazinamide R pncA c.-11A>G (0.14)
Streptomycin R rpsL p.Lys43Arg (0.16), gid c.102delG (0.72)
Fluoroquinolones R gyrA p.Asp94Gly (0.17)
Moxifloxacin R gyrA p.Asp94Gly (0.17)
Ofloxacin R gyrA p.Asp94Gly (0.17)
Levofloxacin R gyrA p.Asp94Gly (0.17)
Ciprofloxacin R gyrA p.Asp94Gly (0.17)
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 0.69
lineage2 East-Asian Beijing RD105 0.29
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.29
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.3
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 0.17 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.31 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.16 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.34 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.14 pyrazinamide
embB 4247729 p.Gly406Ser missense_variant 0.19 ethambutol
gid 4408100 c.102delG frameshift_variant 0.72 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 0.3
ccsA 620625 p.Ile245Met missense_variant 0.36
rpoB 759746 c.-61C>T upstream_gene_variant 0.75
rpoC 762434 c.-936T>G upstream_gene_variant 0.67
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.96
mmpL5 776182 p.Asp767Asn missense_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 0.31
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.34
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.66
pncA 2289365 c.-125delC upstream_gene_variant 0.67
ahpC 2726105 c.-88G>A upstream_gene_variant 0.67
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.25
fbiB 3642627 p.Arg365Gly missense_variant 0.69
alr 3841473 c.-53G>A upstream_gene_variant 0.59
clpC1 4039180 p.Arg509Gly missense_variant 0.66
embC 4242075 p.Arg738Gln missense_variant 0.69
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.3
embB 4247028 p.Leu172Arg missense_variant 0.25
embB 4247033 p.Ser174Arg missense_variant 0.17
embB 4248554 p.Gly681Ser missense_variant 0.63
embB 4249757 p.Thr1082Ala missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 0.31
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.28