TB-Profiler result

Run: ERR4796347

Summary

Run ID: ERR4796347

Sample name:

Date: 20-10-2023 01:43:20

Number of reads: 3658273

Percentage reads mapped: 99.39

Strain: lineage3.1.2.1;lineage2.2.1;lineage1.2.2.2

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 (0.23)
Isoniazid R fabG1 c.-15C>T (0.22), katG p.Ser315Thr (0.17)
Ethambutol R embB p.Gln497Arg (0.12)
Pyrazinamide R pncA p.Gly132Ala (0.24)
Streptomycin R rpsL p.Lys43Arg (0.17)
Fluoroquinolones R gyrA p.Ala90Val (0.16)
Moxifloxacin R gyrA p.Ala90Val (0.16)
Ofloxacin R gyrA p.Ala90Val (0.16)
Levofloxacin R gyrA p.Ala90Val (0.16)
Ciprofloxacin R gyrA p.Ala90Val (0.16)
Aminoglycosides R rrs n.1401A>G (0.36)
Amikacin R rrs n.1401A>G (0.36)
Capreomycin R rrs n.1401A>G (0.36)
Kanamycin R rrs n.1401A>G (0.36), eis c.-10G>C (0.22), eis c.-10G>C (0.22)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.22)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.07
lineage2 East-Asian Beijing RD105 0.17
lineage1 Indo-Oceanic EAI RD239 0.72
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.18
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.73
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.06
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.19
lineage1.2.2.2 Indo-Oceanic NA RD239 0.7
lineage3.1.2.1 East-African-Indian CAS2 RD750 0.08
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 0.16 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.23 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.17 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.36 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.22 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.17 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.24 pyrazinamide
eis 2715342 c.-10G>C upstream_gene_variant 0.22 kanamycin, kanamycin
embB 4248003 p.Gln497Arg missense_variant 0.12 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 5075 c.-165C>T upstream_gene_variant 0.71
gyrB 6112 p.Met291Ile missense_variant 0.76
gyrA 7268 c.-34C>T upstream_gene_variant 0.61
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7773 p.Gly158Ser missense_variant 0.77
gyrA 8452 p.Ala384Val missense_variant 0.75
gyrA 9143 c.1842T>C synonymous_variant 0.67
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.23
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.27
ccsA 620625 p.Ile245Met missense_variant 0.23
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.69
rpoC 763886 c.517C>A synonymous_variant 0.69
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 0.22
mmpS5 779625 c.-720G>A upstream_gene_variant 0.7
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.61
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.23
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 0.73
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156355 c.-244C>T upstream_gene_variant 0.81
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.73
Rv1979c 2222308 p.Asp286Gly missense_variant 0.74
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.68
eis 2714401 p.Ala311Val missense_variant 0.13
ahpC 2726051 c.-142G>A upstream_gene_variant 0.65
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.76
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.8
fprA 3475159 p.Asn385Asp missense_variant 0.66
Rv3236c 3612813 p.Thr102Ala missense_variant 0.2
rpoA 3877750 p.Asp253Gly missense_variant 0.24
rpoA 3878312 p.Val66Leu missense_variant 0.72
clpC1 4040517 p.Val63Ala missense_variant 0.66
clpC1 4040719 c.-15A>G upstream_gene_variant 0.77
embC 4240671 p.Thr270Ile missense_variant 0.76
embC 4241022 p.Ala387Val missense_variant 0.23
embC 4241042 p.Asn394Asp missense_variant 0.75
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.19
embA 4245969 p.Pro913Ser missense_variant 0.71
embB 4247646 p.Glu378Ala missense_variant 0.71
aftB 4267647 p.Asp397Gly missense_variant 0.21
aftB 4267960 p.Val293Met missense_variant 0.66
ubiA 4269387 p.Glu149Asp missense_variant 0.68
aftB 4269606 c.-770T>C upstream_gene_variant 0.78
ethA 4326148 c.1326G>T synonymous_variant 0.76
ethA 4326439 p.Asn345Lys missense_variant 0.77
whiB6 4338203 p.Arg107Cys missense_variant 0.69
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.66
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.23
gid 4407724 p.Leu160Arg missense_variant 0.13
gid 4407848 p.Ala119Thr missense_variant 0.72
gid 4407873 c.330G>T synonymous_variant 0.71
gid 4407927 p.Glu92Asp missense_variant 0.13