TB-Profiler result

Run: SRR25827363

Summary

Run ID: SRR25827363

Sample name:

Date: 01-02-2024 03:23:35

Number of reads: 23241326

Percentage reads mapped: 88.37

Strain: lineage3;lineage2.2.1

Drug-resistance: MDR-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 (0.86)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.17)
Pyrazinamide R pncA p.Gly132Ala (0.18), pncA p.Leu27Pro (0.15), pncA p.Asp12Glu (0.36)
Streptomycin R rpsL p.Lys43Arg (0.14), gid c.351delG (0.20)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides R rrs n.1401A>G (0.43)
Amikacin R rrs n.1401A>G (0.43)
Capreomycin R rrs n.1401A>G (0.43)
Kanamycin R rrs n.1401A>G (0.43)
Cycloserine
Ethionamide R ethA c.1152dupT (0.39), ethA c.1152dupT (0.39), ethA c.87delC (0.24), ethA c.87delC (0.24)
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 0.71
lineage2 East-Asian Beijing RD105 0.29
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.3
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.33
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
rpoB 761155 p.Ser450Leu missense_variant 0.86 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.14 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.43 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.18 pyrazinamide
pncA 2289162 p.Leu27Pro missense_variant 0.15 pyrazinamide
pncA 2289206 p.Asp12Glu missense_variant 0.36 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.17 ethambutol
ethA 4326321 c.1152dupT frameshift_variant 0.39 ethionamide, ethionamide
ethA 4327386 c.87delC frameshift_variant 0.24 ethionamide, ethionamide
gid 4407851 c.351delG frameshift_variant 0.2 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 7581 p.Asp94Cys missense_variant 0.22
gyrA 7585 p.Ser95Thr missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.34
rpoB 759746 c.-61C>T upstream_gene_variant 0.66
rpoC 762434 c.-936T>G upstream_gene_variant 0.61
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766466 p.Glu1033Lys missense_variant 0.42
rpoC 766488 p.Pro1040Arg missense_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.21
mmpS5 779615 c.-710C>G upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.3
embR 1416814 c.534G>A synonymous_variant 0.24
embR 1417190 p.Asp53Gly missense_variant 0.31
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rrs 1473368 n.1523G>A non_coding_transcript_exon_variant 0.19
rpsA 1834177 c.636A>C synonymous_variant 0.34
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
Rv1979c 2222700 c.465C>T synonymous_variant 0.46
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.72
pncA 2289365 c.-125delC upstream_gene_variant 0.69
ahpC 2726105 c.-88G>A upstream_gene_variant 0.68
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 0.26
Rv3236c 3612813 p.Thr102Ala missense_variant 0.29
alr 3841473 c.-53G>A upstream_gene_variant 0.37
panD 4044023 c.259C>T synonymous_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 0.73
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.28
aftB 4267492 p.Ala449Thr missense_variant 0.4
aftB 4267647 p.Asp397Gly missense_variant 0.4
ethA 4326676 p.Ser266Arg missense_variant 0.15
ethA 4326762 p.Val238Ile missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.21
gid 4407967 p.Leu79Trp missense_variant 0.55