TB-Profiler result

Run: SRR25827451
Summary

Run ID: SRR25827451

Sample name:

Date: 02-02-2024 03:58:45

Number of reads: 7011338

Percentage reads mapped: 99.14

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 0.24
lineage4 Euro-American LAM;T;S;X;H None 0.77
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.74
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 0.2
gyrA 9304 p.Gly668Asp missense_variant 0.21
fgd1 491742 c.960T>C synonymous_variant 0.23
rpoB 759746 c.-61C>T upstream_gene_variant 0.31
rpoC 762434 c.-936T>G upstream_gene_variant 0.21
rpoC 763031 c.-339T>C upstream_gene_variant 0.23
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.28
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304938 p.Glu670Gln missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.82
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.23
PPE35 2167926 p.Leu896Ser missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.23
pncA 2289365 c.-125delC upstream_gene_variant 0.2
ahpC 2726105 c.-88G>A upstream_gene_variant 0.27
ahpC 2726561 c.369T>C synonymous_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.29
whiB7 3568425 c.255T>G synonymous_variant 0.18
Rv3236c 3612450 p.Leu223Val missense_variant 0.26
embC 4242075 p.Arg738Gln missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245835 p.Leu868Arg missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.32
gid 4408273 c.-72delG upstream_gene_variant 0.75