TB-Profiler result

Run: ERR181881
Summary

Run ID: ERR181881

Sample name:

Date: 20-10-2023 22:36:48

Number of reads: 3182913

Percentage reads mapped: 97.03

Strain: lineage4.3.4.2.1;lineage3.1.1

Drug-resistance: Other

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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 R rrs n.277G>C (0.15)
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 0.09
lineage4 Euro-American LAM;T;S;X;H None 0.87
lineage4.3 Euro-American (LAM) mainly-LAM None 0.88
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.11
lineage4.3.4 Euro-American (LAM) LAM RD174 0.87
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.89
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
rrs 1472122 n.277G>C non_coding_transcript_exon_variant 0.15 streptomycin
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 6140 p.Val301Leu missense_variant 0.86
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 0.87
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.15
mmpL5 776311 p.Gly724Ser missense_variant 0.79
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.13
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.13
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.15
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.15
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.15
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.14
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.14
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.2
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.2
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.22
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.21
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.21
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.21
pncA 2289365 c.-125delC upstream_gene_variant 0.16
thyA 3073868 p.Thr202Ala missense_variant 0.73
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.86
Rv3236c 3612865 p.Ser84Arg missense_variant 0.72
alr 3840719 c.702A>G synonymous_variant 0.87
clpC1 4038287 c.2418C>T synonymous_variant 0.9
embC 4242075 p.Arg738Gln missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.11
gid 4407991 p.Gly71Val missense_variant 0.14
gid 4408156 p.Leu16Arg missense_variant 0.94