TB-Profiler result

Run: SRR25827703

Summary

Run ID: SRR25827703

Sample name:

Date: 02-02-2024 15:40:07

Number of reads: 9548529

Percentage reads mapped: 92.8

Strain: lineage4.8;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 0.5
lineage4 Euro-American LAM;T;S;X;H None 0.47
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.47
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 5910 p.Ser224Asn missense_variant 0.52
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.51
gyrA 9304 p.Gly668Asp missense_variant 0.52
fgd1 491742 c.960T>C synonymous_variant 0.49
rpoB 759746 c.-61C>T upstream_gene_variant 0.53
rpoC 762434 c.-936T>G upstream_gene_variant 0.5
rpoC 763031 c.-339T>C upstream_gene_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.54
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 0.53
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.46
PPE35 2167926 p.Leu896Ser missense_variant 0.49
PPE35 2168149 p.Pro822Ser missense_variant 0.51
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.53
ahpC 2726105 c.-88G>A upstream_gene_variant 0.53
ald 3086788 c.-32T>C upstream_gene_variant 0.54
ald 3086987 p.Gln56His missense_variant 0.49
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.51
fbiB 3642877 p.Lys448Arg missense_variant 0.53
clpC1 4039729 p.Asp326Asn missense_variant 0.46
embC 4242075 p.Arg738Gln missense_variant 0.48
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 0.46