TB-Profiler result

Run: ERR4798336
Summary

Run ID: ERR4798336

Sample name:

Date: 20-10-2023 02:48:42

Number of reads: 3388398

Percentage reads mapped: 99.4

Strain: lineage3;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.Asp435Tyr (0.71), rpoB p.Ser450Leu (0.28)
Isoniazid R fabG1 c.-17G>T (0.49), katG p.Ser315Thr (1.00), ahpC p.Glu76Lys (0.53)
Ethambutol R embB p.Met306Leu (0.49), embB p.Gln497Arg (0.49)
Pyrazinamide R pncA p.Ala143Pro (0.47)
Streptomycin
Fluoroquinolones R gyrB p.Thr500Asn (0.58), gyrA p.Ser91Pro (0.50)
Moxifloxacin R gyrB p.Thr500Asn (0.58), gyrA p.Ser91Pro (0.50)
Ofloxacin R gyrB p.Thr500Asn (0.58), gyrA p.Ser91Pro (0.50)
Levofloxacin R gyrB p.Thr500Asn (0.58), gyrA p.Ser91Pro (0.50)
Ciprofloxacin R gyrB p.Thr500Asn (0.58), gyrA p.Ser91Pro (0.50)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-17G>T (0.49), ethA p.Pro378Leu (0.48)
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 0.45
lineage1 Indo-Oceanic EAI RD239 0.53
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.53
lineage1.2.2.2 Indo-Oceanic NA RD239 0.52
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
gyrB 6738 p.Thr500Asn missense_variant 0.58 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.5 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 0.71 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.28 rifampicin
fabG1 1673423 c.-17G>T upstream_gene_variant 0.49 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288815 p.Ala143Pro missense_variant 0.47 pyrazinamide
ahpC 2726418 p.Glu76Lys missense_variant 0.53 isoniazid
embB 4247429 p.Met306Leu missense_variant 0.49 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.49 ethambutol
ethA 4326341 p.Pro378Leu missense_variant 0.48 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 5075 c.-165C>T upstream_gene_variant 0.47
gyrB 6112 p.Met291Ile missense_variant 0.51
gyrA 7268 c.-34C>T upstream_gene_variant 0.5
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.45
gyrA 9143 c.1842T>C synonymous_variant 0.44
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.44
rpoC 762434 c.-936T>G upstream_gene_variant 0.54
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.47
rpoC 763886 c.517C>A synonymous_variant 0.47
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779625 c.-720G>A upstream_gene_variant 0.43
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.54
embR 1417040 p.Leu103Pro missense_variant 0.46
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473021 n.1176G>A non_coding_transcript_exon_variant 0.62
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918719 c.780G>A synonymous_variant 0.37
ndh 2102240 p.Arg268His missense_variant 0.51
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.6
Rv1979c 2222308 p.Asp286Gly missense_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.54
pncA 2289365 c.-125delC upstream_gene_variant 0.52
kasA 2518132 c.18C>T synonymous_variant 0.47
ahpC 2726051 c.-142G>A upstream_gene_variant 0.63
ahpC 2726105 c.-88G>A upstream_gene_variant 0.45
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.48
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.48
fprA 3475159 p.Asn385Asp missense_variant 0.49
Rv3236c 3612109 p.Phe336Leu missense_variant 0.53
clpC1 4040517 p.Val63Ala missense_variant 0.5
clpC1 4040719 c.-15A>G upstream_gene_variant 0.57
embC 4240671 p.Thr270Ile missense_variant 0.49
embC 4241042 p.Asn394Asp missense_variant 0.51
embC 4242075 p.Arg738Gln missense_variant 0.44
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243228 c.-5G>A upstream_gene_variant 0.44
embA 4245969 p.Pro913Ser missense_variant 0.54
embB 4246430 c.-84C>T upstream_gene_variant 0.52
embB 4247646 p.Glu378Ala missense_variant 0.52
aftB 4267960 p.Val293Met missense_variant 0.53
ubiA 4269387 p.Glu149Asp missense_variant 0.55
aftB 4269606 c.-770T>C upstream_gene_variant 0.56
ethA 4326148 c.1326G>T synonymous_variant 0.53
ethA 4326439 p.Asn345Lys missense_variant 0.52
whiB6 4338203 p.Arg107Cys missense_variant 0.59
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.54
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407848 p.Ala119Thr missense_variant 0.48
gid 4407873 c.330G>T synonymous_variant 0.5
gid 4408060 p.His48Pro missense_variant 0.48
gid 4408072 p.Leu44Pro missense_variant 0.53