TB-Profiler result

Run: ERR4830361
Summary

Run ID: ERR4830361

Sample name:

Date: 20-10-2023 13:09:22

Number of reads: 3639510

Percentage reads mapped: 98.39

Strain: lineage2.2.1;lineage1.2.1.2.1

Drug-resistance: MDR-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.Val170Phe (0.22), rpoB p.Lys446Gln (0.29)
Isoniazid R fabG1 c.-15C>T (0.20)
Ethambutol R embB p.Asp354Ala (0.27)
Pyrazinamide R pncA c.-11A>G (0.27)
Streptomycin R rpsL p.Lys88Arg (0.24)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (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 0.23
lineage1 Indo-Oceanic EAI RD239 0.77
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.23
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.22
lineage1.2.1 Indo-Oceanic EAI2 RD239 0.8
lineage1.2.1.2 Indo-Oceanic NA RD239 0.75
lineage1.2.1.2.1 Indo-Oceanic NA RD239 0.8
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
rpoB 760314 p.Val170Phe missense_variant 0.22 rifampicin
rpoB 761142 p.Lys446Gln missense_variant 0.29 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.24 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.2 isoniazid, ethionamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.27 pyrazinamide
embB 4247574 p.Asp354Ala missense_variant 0.27 ethambutol
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 6112 p.Met291Ile missense_variant 0.8
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.81
gyrA 9143 c.1842T>C synonymous_variant 0.74
gyrA 9260 c.1959G>C synonymous_variant 0.79
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 0.78
mshA 575907 p.Ala187Val missense_variant 0.36
ccsA 620625 p.Ile245Met missense_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 0.79
rpoC 763884 p.Ala172Val missense_variant 0.85
rpoC 763886 c.517C>A synonymous_variant 0.85
rpoC 765846 p.Asn826Thr missense_variant 0.23
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406312 c.1029T>C synonymous_variant 0.79
Rv1258c 1406760 c.580_581insC frameshift_variant 0.2
embR 1417019 p.Cys110Tyr missense_variant 0.82
atpE 1460907 c.-138T>C upstream_gene_variant 0.74
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.79
inhA 1674162 c.-40C>T upstream_gene_variant 0.78
rpsA 1834177 c.636A>C synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155001 p.Pro371Ser missense_variant 0.23
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 0.81
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.8
kasA 2519048 p.Gly312Ser missense_variant 0.88
ahpC 2726051 c.-142G>A upstream_gene_variant 0.81
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 0.69
Rv3083 3448714 p.Asp71His missense_variant 0.8
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.78
fprA 3475159 p.Asn385Asp missense_variant 0.89
whiB7 3568488 c.191delG frameshift_variant 0.84
Rv3236c 3612813 p.Thr102Ala missense_variant 0.22
fbiB 3640557 c.-978T>C upstream_gene_variant 0.73
clpC1 4040517 p.Val63Ala missense_variant 0.83
embC 4240671 p.Thr270Ile missense_variant 0.83
embC 4241042 p.Asn394Asp missense_variant 0.79
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.15
embA 4243580 c.348G>A synonymous_variant 0.76
embA 4243694 c.462T>C synonymous_variant 0.14
embA 4244420 c.1188G>C synonymous_variant 0.93
embA 4245969 p.Pro913Ser missense_variant 0.63
embB 4247578 c.1065G>A synonymous_variant 0.73
embB 4247646 p.Glu378Ala missense_variant 0.88
aftB 4267647 p.Asp397Gly missense_variant 0.14
ubiA 4269387 p.Glu149Asp missense_variant 0.77
aftB 4269606 c.-770T>C upstream_gene_variant 0.75
ubiA 4269864 c.-32delG upstream_gene_variant 0.81
ethA 4327085 p.Thr130Asn missense_variant 0.23
whiB6 4338361 p.Arg54Gln missense_variant 0.79
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.79
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.83
gid 4407927 p.Glu92Asp missense_variant 0.18