TB-Profiler result

Run: ERR4797417
Summary

Run ID: ERR4797417

Sample name:

Date: 20-10-2023 02:21:10

Number of reads: 3735416

Percentage reads mapped: 99.55

Strain: lineage4.1.1.1;lineage2.2.1.1

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.Ser450Leu (0.23)
Isoniazid R katG p.Ser315Thr (0.34)
Ethambutol R embB p.Met306Val (0.37)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.27)
Fluoroquinolones R gyrA p.Asp94Gly (0.22)
Moxifloxacin R gyrA p.Asp94Gly (0.22)
Ofloxacin R gyrA p.Asp94Gly (0.22)
Levofloxacin R gyrA p.Asp94Gly (0.22)
Ciprofloxacin R gyrA p.Asp94Gly (0.22)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.1242delT (0.20), ethA c.1242delT (0.20), ethA c.754_755dupGC (0.12), ethA c.754_755dupGC (0.12)
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 0.73
lineage4.1 Euro-American T;X;H None 0.75
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.22
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.26
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.76
lineage4.1.1.1 Euro-American (X-type) X2 RD183 0.7
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.23
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 0.22 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.23 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.27 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.34 isoniazid
embB 4247429 p.Met306Val missense_variant 0.37 ethambutol
ethA 4326231 c.1242delT frameshift_variant 0.2 ethionamide, ethionamide
ethA 4326718 c.754_755dupGC frameshift_variant 0.12 ethionamide, ethionamide
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 5936 p.Ala233Pro missense_variant 0.1
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 491742 c.960T>C synonymous_variant 0.23
mshA 575907 p.Ala187Val missense_variant 0.24
ccsA 620625 p.Ile245Met missense_variant 0.22
rpoB 761292 p.Val496Met missense_variant 0.13
rpoC 764363 p.Gly332Ser missense_variant 0.13
rpoC 765150 p.Gly594Glu missense_variant 0.78
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.25
mmpL5 776182 p.Asp767Asn missense_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 0.27
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.24
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.27
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.28
PPE35 2167926 p.Leu896Ser missense_variant 0.25
PPE35 2167967 c.2645dupC frameshift_variant 0.76
PPE35 2168034 p.Thr860Ile missense_variant 0.74
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_variant 0.24
thyA 3074282 p.Arg64Cys missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 0.9
ald 3087711 p.Val298Met missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.22
fbiB 3641238 c.-297G>A upstream_gene_variant 0.66
fbiA 3641447 p.Thr302Met missense_variant 0.77
rpoA 3877553 p.Glu319Lys missense_variant 0.67
embC 4240897 c.1035C>G synonymous_variant 0.79
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.68
embA 4243460 c.228C>T synonymous_variant 0.17
embB 4246746 p.Asp78Gly missense_variant 0.74
embB 4247880 p.Val456Ala missense_variant 0.29
embB 4248115 c.1602C>T synonymous_variant 0.4
embB 4249408 c.2895G>A synonymous_variant 0.76
aftB 4267647 p.Asp397Gly missense_variant 0.14
ubiA 4269245 p.His197Tyr missense_variant 0.73
whiB6 4338410 p.Pro38Ala missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.17
gid 4407927 p.Glu92Asp missense_variant 0.26
gid 4408266 c.-64C>G upstream_gene_variant 0.1