TB-Profiler result

Run: ERR4799921
Summary

Run ID: ERR4799921

Sample name:

Date: 20-10-2023 03:55:16

Number of reads: 3752205

Percentage reads mapped: 99.6

Strain: lineage4.8;lineage3.1.2

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys88Arg (0.48), gid c.351delG (0.11)
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 0.45
lineage4 Euro-American LAM;T;S;X;H None 0.58
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.57
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.39
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.44
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
rpsL 781822 p.Lys88Arg missense_variant 0.48 streptomycin
gid 4407851 c.351delG frameshift_variant 0.11 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
gyrA 7362 p.Glu21Gln missense_variant 0.99
gyrA 7585 p.Ser95Thr missense_variant 0.57
gyrA 8741 c.1440C>T synonymous_variant 0.23
gyrA 9304 p.Gly668Asp missense_variant 0.53
fgd1 491742 c.960T>C synonymous_variant 0.45
ccsA 620418 c.528G>A synonymous_variant 0.51
rpoB 759746 c.-61C>T upstream_gene_variant 0.48
rpoC 762434 c.-936T>G upstream_gene_variant 0.4
rpoC 763031 c.-339T>C upstream_gene_variant 0.47
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.49
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473543 n.-115C>T upstream_gene_variant 0.44
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.53
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.52
katG 2156482 c.-371G>A upstream_gene_variant 0.39
PPE35 2167926 p.Leu896Ser missense_variant 0.43
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.98
pncA 2289047 c.195C>T synonymous_variant 0.41
pncA 2289365 c.-125delC upstream_gene_variant 0.5
eis 2714222 p.Ala371Ser missense_variant 0.57
ahpC 2726105 c.-88G>A upstream_gene_variant 0.49
ald 3086788 c.-32T>C upstream_gene_variant 0.56
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.39
panD 4044340 c.-59G>T upstream_gene_variant 0.47
embC 4242075 p.Arg738Gln missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249699 c.3186T>C synonymous_variant 0.44
aftB 4267364 p.Met491Ile missense_variant 0.39
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.46
gid 4408047 p.Cys52Trp missense_variant 0.2