TB-Profiler result

Run: ERR8025574

Summary

Run ID: ERR8025574

Sample name:

Date: 18-05-2023 02:29:57

Number of reads: 2546879

Percentage reads mapped: 99.59

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), katG p.Ala106Val (0.11)
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), ethA p.Gln121* (0.20)
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
katG 2155795 p.Ala106Val missense_variant 0.11 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
ethA 4327113 p.Gln121* stop_gained 0.2 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 7781 c.480G>C synonymous_variant 0.2
gyrA 8616 p.Gln439* stop_gained 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576461 p.Ala372Thr missense_variant 0.12
rpoB 760030 c.227delC frameshift_variant 0.14
rpoB 760794 p.Glu330Gln missense_variant 0.12
rpoB 761213 c.1407G>A synonymous_variant 0.14
rpoB 762124 p.Glu773Gly missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 1.0
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 1303593 c.663G>A synonymous_variant 0.13
fbiC 1303990 c.1064dupG frameshift_variant 0.15
fbiC 1305345 c.2415C>T synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673744 p.Glu102Ala missense_variant 0.12
inhA 1674686 p.Thr162Met missense_variant 0.18
rpsA 1833969 p.Gly143Glu missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917838 c.-102G>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917989 p.Ala17Val missense_variant 0.11
ndh 2102859 c.183delG frameshift_variant 0.11
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 2222417 c.748C>A synonymous_variant 0.12
Rv1979c 2222443 p.Ala241Asp missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288918 c.324A>T synonymous_variant 0.12
kasA 2518592 c.481delC frameshift_variant 0.14
ahpC 2726221 c.33delC frameshift_variant 0.11
folC 2746524 p.Ala359Ser missense_variant 0.12
folC 2747108 p.Ala164Val missense_variant 0.17
pepQ 2860199 p.Ala74Thr missense_variant 0.11
thyX 3067223 c.723G>A synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449017 p.Asp172Tyr missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475085 p.Ile360Asn missense_variant 0.14
fprA 3475258 p.Val418Ile missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641448 c.-87G>A upstream_gene_variant 0.13
fbiB 3641463 c.-72G>A upstream_gene_variant 0.13
rpoA 3878622 c.-115C>A upstream_gene_variant 0.12
clpC1 4038901 p.Val602Ile missense_variant 0.14
embC 4241210 p.Leu450Val missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243210 c.-23C>T upstream_gene_variant 0.11
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244239 p.Trp336* stop_gained 0.14
embA 4244249 c.1018delA frameshift_variant 0.12
embB 4246563 p.Leu17Trp missense_variant 0.1
embB 4248054 p.Pro514Leu missense_variant 0.12
embB 4249221 p.Ala903Val missense_variant 0.11
embB 4249476 p.Trp988Leu missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268086 c.750delG frameshift_variant 0.15
aftB 4268625 p.Gly71Asp missense_variant 0.11
ubiA 4269077 p.Ile253Val missense_variant 0.1
ubiA 4269089 p.Ala249Thr missense_variant 1.0
ubiA 4269137 p.Tyr233His missense_variant 0.11
ethA 4327957 c.-484G>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