TB-Profiler result

Run: SRR25827376

Summary

Run ID: SRR25827376

Sample name:

Date: 01-02-2024 05:15:31

Number of reads: 16848810

Percentage reads mapped: 98.86

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.Ser428Gly (0.88), rpoB p.Leu452Pro (0.90)
Isoniazid R katG p.Ser315Thr (0.90)
Ethambutol R embA c.-16C>T (0.80)
Pyrazinamide R pncA p.Gly132Ser (0.82)
Streptomycin R rpsL p.Lys43Arg (0.92)
Fluoroquinolones R gyrA p.Asp94Gly (0.11)
Moxifloxacin R gyrA p.Asp94Gly (0.11)
Ofloxacin R gyrA p.Asp94Gly (0.11)
Levofloxacin R gyrA p.Asp94Gly (0.11)
Ciprofloxacin R gyrA p.Asp94Gly (0.11)
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 0.08
lineage2 East-Asian Beijing RD105 0.91
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.87
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.89
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 0.11 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761088 p.Ser428Gly missense_variant 0.88 rifampicin
rpoB 761161 p.Leu452Pro missense_variant 0.9 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.92 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.9 isoniazid
pncA 2288848 p.Gly132Ser missense_variant 0.82 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.8 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 491290 p.Val170Met missense_variant 0.87
fgd1 491742 c.960T>C synonymous_variant 0.98
mshA 575907 p.Ala187Val missense_variant 0.87
ccsA 620625 p.Ile245Met missense_variant 0.85
rpoB 759746 c.-61C>T upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.98
mmpL5 776182 p.Asp767Asn missense_variant 0.86
mmpS5 779615 c.-710C>G upstream_gene_variant 0.85
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304390 p.Ala487Val missense_variant 0.83
Rv1258c 1406760 c.580_581insC frameshift_variant 0.9
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.85
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 0.97
PPE35 2170048 p.Leu189Val missense_variant 0.52
PPE35 2170053 p.Thr187Ser missense_variant 0.51
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.13
Rv2752c 3065294 c.897delA frameshift_variant 0.81
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.9
embC 4241022 p.Ala387Val missense_variant 0.84
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.85
embB 4246544 p.Thr11Pro missense_variant 0.49
embB 4246548 p.Pro12Gln missense_variant 0.51
embB 4246555 c.42G>C synonymous_variant 0.51
embB 4246556 p.Ala15Pro missense_variant 0.51
embB 4246563 p.Leu17Trp missense_variant 0.51
embB 4246567 c.54G>T synonymous_variant 0.38
embB 4247028 p.Leu172Arg missense_variant 0.21
embB 4247039 p.Phe176Val missense_variant 0.15
embB 4249794 p.Ile1094Ser missense_variant 0.81
aftB 4267647 p.Asp397Gly missense_variant 0.89
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.98
gid 4407620 p.Tyr195His missense_variant 0.84
gid 4407927 p.Glu92Asp missense_variant 0.89