TB-Profiler result

Run: ERR181705

Summary

Run ID: ERR181705

Sample name:

Date: 20-10-2023 22:29:52

Number of reads: 5021110

Percentage reads mapped: 99.64

Strain: lineage4.3.4.2.1;lineage1.2.2.1

Drug-resistance: Sensitive


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 0.86
lineage1 Indo-Oceanic EAI RD239 0.14
lineage4.3 Euro-American (LAM) mainly-LAM None 0.86
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.15
lineage4.3.4 Euro-American (LAM) LAM RD174 0.87
lineage1.2.2.1 Indo-Oceanic NA RD239 0.11
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.85
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.86
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
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 0.16
gyrB 6112 p.Met291Ile missense_variant 0.13
gyrB 6140 p.Val301Leu missense_variant 0.79
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 0.19
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491060 p.Met93Thr missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 0.13
rpoC 763884 p.Ala172Val missense_variant 0.12
rpoC 763886 c.517C>A synonymous_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 0.87
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800799 c.-10G>A upstream_gene_variant 0.11
rplC 800899 p.Ala31Thr missense_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.14
Rv1979c 2222308 p.Asp286Gly missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289346 c.-105A>G upstream_gene_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 0.14
Rv2752c 3067032 c.-841C>G upstream_gene_variant 0.14
thyX 3067245 p.Thr234Asn missense_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 0.87
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.15
Rv3236c 3612009 p.Ala370Thr missense_variant 0.83
alr 3840719 c.702A>G synonymous_variant 0.81
clpC1 4038287 c.2418C>T synonymous_variant 0.88
clpC1 4040517 p.Val63Ala missense_variant 0.15
panD 4044313 c.-32C>T upstream_gene_variant 0.16
embC 4240671 p.Thr270Ile missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 0.12
ethR 4327450 c.-99G>A upstream_gene_variant 0.13
whiB6 4338310 p.Gly71Asp missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.17
gid 4407588 c.615A>G synonymous_variant 0.27
gid 4407873 c.330G>T synonymous_variant 0.21
gid 4408156 p.Leu16Arg missense_variant 0.81