TB-Profiler result

Run: ERR8025721

Summary

Run ID: ERR8025721

Sample name:

Date: 18-05-2023 06:50:39

Number of reads: 2584892

Percentage reads mapped: 99.57

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 0.99
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
gyrB 6355 p.Lys372Asn missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8774 c.1473C>A synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491100 c.318C>T synonymous_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575966 p.Val207Phe missense_variant 0.2
mshA 576161 p.Gly272Arg missense_variant 0.13
rpoB 761288 c.1482G>A synonymous_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 766798 c.3429C>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777965 c.516C>T synonymous_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800824 p.Ile6Val missense_variant 0.11
fbiC 1303152 c.222C>T synonymous_variant 0.14
Rv1258c 1406940 p.Arg134Gln missense_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673349 c.-91G>A upstream_gene_variant 0.13
inhA 1673466 c.-736C>A upstream_gene_variant 0.14
fabG1 1673624 p.Val62Asp missense_variant 0.11
rpsA 1833691 p.Glu50Asp missense_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834540 c.1002delC frameshift_variant 0.13
tlyA 1917779 c.-161C>T upstream_gene_variant 0.15
tlyA 1917804 c.-136G>T upstream_gene_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103213 c.-171G>T upstream_gene_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156057 p.Gly19Ser missense_variant 0.12
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
kasA 2518474 p.Glu120Asp missense_variant 0.11
kasA 2519236 p.Glu374Asp missense_variant 0.12
pepQ 2859939 c.480C>T synonymous_variant 0.18
Rv2752c 3064589 p.Arg535Ser missense_variant 0.12
thyX 3067193 c.753A>G stop_lost&splice_region_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473843 c.-164C>T upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474543 c.537C>G synonymous_variant 0.14
fprA 3475374 c.1368C>T synonymous_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642023 c.489C>A synonymous_variant 0.14
fbiB 3642378 p.Glu282* stop_gained 0.25
panD 4044066 c.216C>T synonymous_variant 0.15
panD 4044251 p.His11Tyr missense_variant 0.25
embC 4241796 p.Asn645Ser missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248583 c.2070C>A synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269089 p.Ala249Thr missense_variant 1.0
ethA 4326858 p.Gln206Glu missense_variant 0.13
ethA 4328253 c.-780C>A upstream_gene_variant 0.12
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