TB-Profiler result

Run: ERR2514501

Summary

Run ID: ERR2514501

Sample name:

Date: 20-10-2023 12:04:46

Number of reads: 1577113

Percentage reads mapped: 99.41

Strain: lineage4.4;lineage4.3.4.2.1;lineage1.1.2

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 0.45
lineage1 Indo-Oceanic EAI RD239 0.48
lineage4.3 Euro-American (LAM) mainly-LAM None 0.26
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.52
lineage4.4 Euro-American S;T None 0.19
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.48
lineage4.3.4 Euro-American (LAM) LAM RD174 0.27
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.25
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.27
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 6112 p.Met291Ile missense_variant 0.49
gyrB 6124 c.885C>T synonymous_variant 0.49
gyrB 6140 p.Val301Leu missense_variant 0.21
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.56
gyrA 9143 c.1842T>C synonymous_variant 0.43
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.44
rpoB 760490 c.684C>T synonymous_variant 0.52
rpoB 762368 c.2562G>A synonymous_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 0.57
rpoC 763884 p.Ala172Val missense_variant 0.4
rpoC 763886 c.517C>A synonymous_variant 0.41
rpoC 764995 c.1626C>G synonymous_variant 0.23
rpoC 765171 p.Pro601Leu missense_variant 0.45
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.43
mmpL5 776395 p.Phe696Leu missense_variant 0.52
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.55
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476121 n.2464C>A non_coding_transcript_exon_variant 0.23
fabG1 1673280 c.-160C>T upstream_gene_variant 0.32
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101955 p.Gln363Ser missense_variant 0.45
katG 2154724 p.Arg463Leu missense_variant 0.52
PPE35 2167701 p.Ala971Gly missense_variant 0.46
PPE35 2167926 p.Leu896Ser missense_variant 0.46
PPE35 2167983 p.Gly877Asp missense_variant 0.45
Rv1979c 2222308 p.Asp286Gly missense_variant 0.42
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.55
ahpC 2726051 c.-142G>A upstream_gene_variant 0.33
Rv2752c 3064632 c.1560C>T synonymous_variant 0.53
thyA 3073868 p.Thr202Ala missense_variant 0.32
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.54
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.55
fprA 3475159 p.Asn385Asp missense_variant 0.61
Rv3236c 3612009 p.Ala370Thr missense_variant 0.25
alr 3840719 c.702A>G synonymous_variant 0.34
clpC1 4038287 c.2418C>T synonymous_variant 0.34
clpC1 4040517 p.Val63Ala missense_variant 0.43
embC 4240671 p.Thr270Ile missense_variant 0.74
embC 4241005 c.1143G>C synonymous_variant 0.47
embC 4241042 p.Asn394Asp missense_variant 0.51
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.57
embA 4245218 c.1986C>T synonymous_variant 0.64
embA 4245969 p.Pro913Ser missense_variant 0.47
embB 4247646 p.Glu378Ala missense_variant 0.37
aftB 4267118 c.1719G>A synonymous_variant 0.14
aftB 4268928 c.-92C>T upstream_gene_variant 0.32
ubiA 4269031 p.Gly268Asp missense_variant 0.46
aftB 4269375 c.-539G>A upstream_gene_variant 0.2
ubiA 4269387 p.Glu149Asp missense_variant 0.55
aftB 4269606 c.-770T>C upstream_gene_variant 0.49
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.49
gid 4407588 c.615A>G synonymous_variant 0.45
gid 4407873 c.330G>T synonymous_variant 0.6
gid 4408156 p.Leu16Arg missense_variant 0.23