TB-Profiler result

Run: SRR25827563
Summary

Run ID: SRR25827563

Sample name:

Date: 15-02-2024 06:06:59

Number of reads: 8074936

Percentage reads mapped: 99.08

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 (0.82)
Isoniazid R katG p.Ile317Val (0.13), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.41), embB p.His1002Arg (0.14)
Pyrazinamide R pncA p.Leu27Pro (0.28)
Streptomycin R rpsL p.Lys43Arg (0.50)
Fluoroquinolones R gyrA p.Asp94Gly (0.48)
Moxifloxacin R gyrA p.Asp94Gly (0.48)
Ofloxacin R gyrA p.Asp94Gly (0.48)
Levofloxacin R gyrA p.Asp94Gly (0.48)
Ciprofloxacin R gyrA p.Asp94Gly (0.48)
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 0.21
lineage2 East-Asian Beijing RD105 0.74
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.74
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.75
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.17
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 0.48 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.82 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.5 streptomycin
katG 2155163 p.Ile317Val missense_variant 0.13 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 0.28 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.41 ethambutol
embB 4249518 p.His1002Arg missense_variant 0.14 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 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 0.35
ccsA 620625 p.Ile245Met missense_variant 0.62
rpoB 759746 c.-61C>T upstream_gene_variant 0.22
rpoC 762434 c.-936T>G upstream_gene_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.97
mmpL5 776182 p.Asp767Asn missense_variant 0.33
mmpS5 779615 c.-710C>G upstream_gene_variant 0.76
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.72
rrs 1471659 n.-187C>T upstream_gene_variant 0.93
rrs 1471871 n.26C>T non_coding_transcript_exon_variant 0.17
rrl 1473609 n.-49G>C upstream_gene_variant 0.21
inhA 1673406 c.-796C>G upstream_gene_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 0.74
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.98
PPE35 2167802 c.2810delG frameshift_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 0.94
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.22
pncA 2289365 c.-125delC upstream_gene_variant 0.24
kasA 2518980 p.Arg289Thr missense_variant 0.15
eis 2714846 p.Val163Ile missense_variant 0.2
folC 2747504 p.His32Arg missense_variant 0.2
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 0.73
fbiB 3640879 c.-656C>T upstream_gene_variant 0.18
rpoA 3877960 p.Val183Gly missense_variant 0.14
embC 4242056 p.Pro732Ala missense_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.72
embB 4247028 p.Leu172Arg missense_variant 0.21
embB 4248115 c.1602C>T synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 0.76
ethA 4326474 p.Pro334Ala missense_variant 0.16
ethA 4326676 p.Ser266Arg missense_variant 0.18
ethA 4326735 p.Ala247Pro missense_variant 0.2
whiB6 4338233 p.Ser97Pro missense_variant 0.16
whiB6 4338293 p.Ala77Ser missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.95
gid 4407927 p.Glu92Asp missense_variant 0.77