TB-Profiler result

Run: SRR25340778
Summary

Run ID: SRR25340778

Sample name:

Date: 28-01-2024 23:50:47

Number of reads: 6146934

Percentage reads mapped: 99.44

Strain: lineage4.8;lineage3.1.2

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
lineage3 East-African-Indian CAS RD750 0.65
lineage4 Euro-American LAM;T;S;X;H None 0.38
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.33
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.62
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.71
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 0.71
gyrA 9304 p.Gly668Asp missense_variant 0.65
fgd1 490935 c.153C>T synonymous_variant 0.3
fgd1 491742 c.960T>C synonymous_variant 0.7
rpoB 759746 c.-61C>T upstream_gene_variant 0.67
rpoC 762434 c.-936T>G upstream_gene_variant 0.65
rpoC 763031 c.-339T>C upstream_gene_variant 0.68
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.67
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.35
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918104 c.165G>A synonymous_variant 0.64
katG 2154724 p.Arg463Leu missense_variant 0.69
katG 2155697 p.Ala139Thr missense_variant 0.63
PPE35 2167926 p.Leu896Ser missense_variant 0.74
PPE35 2168604 p.Pro670Leu missense_variant 0.71
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.76
pncA 2289365 c.-125delC upstream_gene_variant 0.78
kasA 2517923 c.-192C>T upstream_gene_variant 0.43
ahpC 2726105 c.-88G>A upstream_gene_variant 0.72
ald 3086788 c.-32T>C upstream_gene_variant 0.68
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.64
embC 4240966 c.1104G>A synonymous_variant 0.42
embC 4242075 p.Arg738Gln missense_variant 0.51
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338472 p.Arg17Lys missense_variant 0.62
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.66