TB-Profiler result

Run: ERR8025666
Summary

Run ID: ERR8025666

Sample name:

Date: 18-05-2023 05:07:55

Number of reads: 2447106

Percentage reads mapped: 99.59

Strain: lineage2.2.2

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Asp435Val (1.00)
Isoniazid R fabG1 c.-17G>T (1.00), katG c.1471_1472delGG (0.11), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA c.517dupG (1.00), pncA c.517dupG (1.00), pncA c.74_75delCC (0.10)
Streptomycin R rrs n.514A>C (1.00), gid p.Leu79Ser (1.00)
Fluoroquinolones R gyrA p.Asp94Asn (1.00)
Moxifloxacin R gyrA p.Asp94Asn (1.00)
Ofloxacin R gyrA p.Asp94Asn (1.00)
Levofloxacin R gyrA p.Asp94Asn (1.00)
Ciprofloxacin R gyrA p.Asp94Asn (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 R alr p.Leu113Arg (1.00)
Ethionamide R fabG1 c.-17G>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 7581 p.Asp94Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val 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 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2154639 c.1471_1472delGG frameshift_variant 0.11 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288724 c.517dupG frameshift_variant 1.0 pyrazinamide, pyrazinamide
pncA 2289166 c.74_75delCC frameshift_variant 0.1 pyrazinamide
alr 3841083 p.Leu113Arg missense_variant 1.0 cycloserine
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491723 p.Gly314Glu missense_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575435 p.Pro30Ser missense_variant 0.12
rpoB 762328 p.Val841Ala missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763724 p.Asp119Asn missense_variant 0.12
rpoC 764526 p.Arg386His missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304685 c.1755C>T synonymous_variant 0.13
atpE 1461068 c.24C>T synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918217 p.Thr93Ile missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221869 c.1296C>T synonymous_variant 0.12
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2222796 c.369C>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288968 p.Ala92Thr missense_variant 0.12
eis 2715433 c.-101T>A upstream_gene_variant 0.12
folC 2747167 p.Lys144Asn missense_variant 0.13
pepQ 2860218 c.201A>G synonymous_variant 0.11
ribD 2987496 p.Val220Ile missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474672 c.666C>T synonymous_variant 0.13
fprA 3475227 c.1221C>T synonymous_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641741 p.Gln69His missense_variant 0.13
clpC1 4039946 c.759A>G synonymous_variant 0.11
panD 4044237 c.45G>A synonymous_variant 0.12
embC 4240591 c.729C>T synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242804 p.Val981Ala missense_variant 0.11
embC 4242872 p.Asp1004Asn missense_variant 0.12
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246655 p.Pro48Thr missense_variant 0.15
embB 4246937 c.428delC frameshift_variant 0.14
aftB 4267647 p.Asp397Gly 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 1.0