TB-Profiler result

Run: ERR8025689
Summary

Run ID: ERR8025689

Sample name:

Date: 20-05-2023 20:56:34

Number of reads: 2303196

Percentage reads mapped: 99.51

Strain: lineage2.2.2

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)
Isoniazid R fabG1 c.-15C>T (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.Cys14Arg (1.00)
Streptomycin R rrs n.514A>C (1.00), gid p.Leu79Ser (1.00)
Fluoroquinolones R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (1.00)
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), ethA p.Ala381Pro (1.00)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 1.0
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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289202 p.Cys14Arg missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 1.0 ethionamide
gid 4407967 p.Leu79Ser missense_variant 1.0 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 8580 p.Ile427Phe missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490852 p.Ala24Ser missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576370 c.1023G>T synonymous_variant 0.15
ccsA 620173 p.Val95Phe missense_variant 0.15
ccsA 620304 p.Trp138Cys missense_variant 0.14
rpoB 760934 c.1128C>T synonymous_variant 0.14
rpoB 761509 p.Ser568Phe missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 766047 p.Thr893Asn missense_variant 0.12
rpoC 766092 p.Gly908Val missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 0.92
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 778863 p.Leu15Met missense_variant 0.14
mmpL5 778920 c.-440C>A upstream_gene_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781513 c.-47T>C upstream_gene_variant 0.1
rplC 801284 p.Arg159Leu missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673644 p.Asp69Asn missense_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918356 c.417C>A synonymous_variant 0.12
tlyA 1918387 p.Leu150Met missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714842 p.Arg164Gln missense_variant 0.13
folC 2746998 p.His201Asn missense_variant 0.12
ribD 2986713 c.-126A>G upstream_gene_variant 0.12
ribD 2987236 c.400_401delAC frameshift_variant 0.17
Rv2752c 3064535 p.Pro553Ser missense_variant 0.12
Rv2752c 3065890 p.Pro101Gln missense_variant 0.12
Rv2752c 3067017 c.-826G>A upstream_gene_variant 0.17
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 1.0
fbiB 3641597 c.63C>A synonymous_variant 0.15
fbiB 3641662 p.Gly43Val missense_variant 0.17
fbiB 3641951 c.417G>A synonymous_variant 0.13
alr 3840240 p.Pro394Leu missense_variant 0.13
rpoA 3877500 c.1008C>T synonymous_variant 0.14
ddn 3987156 c.314_315delAA frameshift_variant 0.12
clpC1 4038181 p.Gly842Ser missense_variant 0.12
clpC1 4038206 c.2499C>A synonymous_variant 0.12
panD 4044453 c.-172G>A upstream_gene_variant 0.14
embC 4240387 c.525C>A synonymous_variant 0.12
embC 4241689 c.1827G>T synonymous_variant 0.14
embC 4241717 p.Arg619Trp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4246009 p.Arg926Leu missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269089 p.Ala249Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.94