TB-Profiler result

Run: ERR8025589

Summary

Run ID: ERR8025589

Sample name:

Date: 23-05-2023 04:28:24

Number of reads: 2752342

Percentage reads mapped: 99.58

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.Asp435Val (1.00)
Isoniazid R fabG1 c.-17G>T (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA c.517dupG (1.00), pncA c.517dupG (1.00)
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 c.1447delA (0.10), 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 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288724 c.517dupG frameshift_variant 1.0 pyrazinamide, pyrazinamide
alr 3841083 p.Leu113Arg missense_variant 1.0 cycloserine
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326026 c.1447delA frameshift_variant 0.1 ethionamide
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 6124 c.888delG frameshift_variant 0.1
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7456 p.His52Leu missense_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575328 c.-20T>C upstream_gene_variant 0.11
mshA 575538 p.Asp64Gly missense_variant 0.15
mshA 575595 p.Gly83Asp missense_variant 0.15
mshA 576204 p.Ala286Val missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 778076 c.-914G>A upstream_gene_variant 0.12
mmpS5 778845 p.Ala21Thr missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406751 p.Gly197Asp missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475151 n.1494C>G non_coding_transcript_exon_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918660 c.721C>T synonymous_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156061 c.51C>T synonymous_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
pepQ 2859573 c.846C>T synonymous_variant 0.11
ribD 2986820 c.-19A>G upstream_gene_variant 0.12
ribD 2987095 p.Gly86Asp missense_variant 0.13
ribD 2987151 p.His105Tyr missense_variant 0.2
ribD 2987516 c.678C>A synonymous_variant 0.11
thyX 3068151 c.-206T>C upstream_gene_variant 0.11
thyA 3074151 c.321G>A synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087254 c.435C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474706 c.702dupC frameshift_variant 0.14
fprA 3474842 p.Lys279Met missense_variant 0.12
fprA 3475078 p.Gly358Arg missense_variant 0.11
Rv3236c 3612806 p.Gly104Asp missense_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612857 p.Arg87His missense_variant 0.2
fbiA 3640777 c.239delG frameshift_variant 0.18
fbiB 3641709 p.Arg59Trp missense_variant 0.17
fbiB 3641742 p.Arg70Gly missense_variant 0.13
alr 3840268 p.Thr385Ser missense_variant 0.14
ddn 3987295 p.Pro151His missense_variant 0.12
clpC1 4038926 c.1779G>A synonymous_variant 0.1
clpC1 4039550 c.1155G>A synonymous_variant 0.13
embC 4240746 p.Gly295Asp missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4246027 p.Ala932Val missense_variant 0.12
embB 4246660 c.147C>T synonymous_variant 0.11
embB 4249801 c.3288T>A synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326121 c.1353G>A synonymous_variant 0.12
whiB6 4338352 p.Pro57Gln missense_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