TB-Profiler result

Run: ERR4818629
Summary

Run ID: ERR4818629

Sample name:

Date: 20-10-2023 08:43:33

Number of reads: 1817991

Percentage reads mapped: 96.54

Strain: lineage4.3.3;lineage3

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
lineage3 East-African-Indian CAS RD750 0.38
lineage4 Euro-American LAM;T;S;X;H None 0.69
lineage4.3 Euro-American (LAM) mainly-LAM None 0.72
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.7
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.59
gyrA 8808 p.Gly503Arg missense_variant 0.55
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.38
rpoB 759746 c.-61C>T upstream_gene_variant 0.35
rpoC 762434 c.-936T>G upstream_gene_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 0.37
rpoC 764995 c.1626C>G synonymous_variant 0.81
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.31
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.47
rrs 1472954 n.1109T>C non_coding_transcript_exon_variant 0.53
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.71
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.65
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.67
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.86
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.64
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.65
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.59
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.56
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.56
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.56
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.56
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.5
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.5
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.38
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.5
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.53
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.53
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.45
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.32
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.35
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.52
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.5
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.35
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.35
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.39
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.38
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.35
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.54
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.54
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.54
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.54
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.67
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.56
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.53
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.71
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.46
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.27
PPE35 2167926 p.Leu896Ser missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.36
pncA 2289365 c.-125delC upstream_gene_variant 0.37
kasA 2518919 p.Gly269Ser missense_variant 0.67
ahpC 2726105 c.-88G>A upstream_gene_variant 0.33
Rv2752c 3066313 c.-122T>G upstream_gene_variant 0.72
thyA 3073868 p.Thr202Ala missense_variant 0.72
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841473 c.-53G>A upstream_gene_variant 0.34
clpC1 4038287 c.2418C>T synonymous_variant 0.6
embC 4242075 p.Arg738Gln missense_variant 0.27
embC 4242182 p.Ala774Ser missense_variant 0.78
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245100 p.Gly623Ala missense_variant 0.58
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.3
gid 4408156 p.Leu16Arg missense_variant 0.68