TB-Profiler result

Run: ERR4813180

Summary

Run ID: ERR4813180

Sample name:

Date: 20-10-2023 05:08:22

Number of reads: 3255208

Percentage reads mapped: 99.7

Strain: lineage4.3.3;lineage2.2.1

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 (0.67), rpoB p.Ser450Leu (0.34)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Tyr319Ser (0.73), embB p.Gly406Ala (0.27)
Pyrazinamide R pncA p.Thr142Ala (0.26), pncA p.Gln10Arg (0.71)
Streptomycin R rpsL p.Lys43Arg (0.26), gid p.Pro84Leu (0.76)
Fluoroquinolones R gyrA p.Ala90Val (0.73), gyrA p.Asp94Tyr (0.14)
Moxifloxacin R gyrA p.Ala90Val (0.73), gyrA p.Asp94Tyr (0.14)
Ofloxacin R gyrA p.Ala90Val (0.73), gyrA p.Asp94Tyr (0.14)
Levofloxacin R gyrA p.Ala90Val (0.73), gyrA p.Asp94Tyr (0.14)
Ciprofloxacin R gyrA p.Ala90Val (0.73), gyrA p.Asp94Tyr (0.14)
Aminoglycosides R rrs n.1401A>G (0.27)
Amikacin R rrs n.1401A>G (0.27)
Capreomycin R rrs n.1401A>G (0.27)
Kanamycin R rrs n.1401A>G (0.27)
Cycloserine
Ethionamide R ethA p.Ser390Phe (0.29), ethA c.752dupG (0.66), ethA c.752dupG (0.66)
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 0.28
lineage4 Euro-American LAM;T;S;X;H None 0.72
lineage4.3 Euro-American (LAM) mainly-LAM None 0.74
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.25
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.3
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.72
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 7570 p.Ala90Val missense_variant 0.73 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94Tyr missense_variant 0.14 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.67 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.34 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.26 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.27 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288818 p.Thr142Ala missense_variant 0.26 pyrazinamide
pncA 2289213 p.Gln10Arg missense_variant 0.71 pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 0.73 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.27 ethambutol
ethA 4326305 p.Ser390Phe missense_variant 0.29 ethionamide
ethA 4326721 c.752dupG frameshift_variant 0.66 ethionamide, ethionamide
gid 4407952 p.Pro84Leu missense_variant 0.76 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 8040 p.Gly247Ser missense_variant 0.7
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.26
mshA 575907 p.Ala187Val missense_variant 0.21
ccsA 620625 p.Ile245Met missense_variant 0.31
rpoC 763031 c.-339T>C upstream_gene_variant 0.3
rpoC 764817 p.Val483Ala missense_variant 0.3
rpoC 764995 c.1626C>G synonymous_variant 0.73
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.3
mmpL5 776182 p.Asp767Asn missense_variant 0.35
mmpS5 779615 c.-710C>G upstream_gene_variant 0.23
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303897 c.967C>T synonymous_variant 0.26
Rv1258c 1406760 c.580_581insC frameshift_variant 0.26
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.27
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 0.66
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.21
PPE35 2167926 p.Leu896Ser missense_variant 0.32
PPE35 2168998 p.Ile539Val missense_variant 0.78
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.71
thyA 3073868 p.Thr202Ala missense_variant 0.71
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087208 p.Leu130Pro missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.26
clpC1 4038287 c.2418C>T synonymous_variant 0.68
embC 4242182 p.Ala774Ser missense_variant 0.73
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 0.23
whiB6 4338473 c.49A>C synonymous_variant 0.28
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.3
gid 4407927 p.Glu92Asp missense_variant 0.18
gid 4408156 p.Leu16Arg missense_variant 0.66
gid 4408413 c.-211C>T upstream_gene_variant 0.33