TB-Profiler result

Run: SRR2101359
Summary

Run ID: SRR2101359

Sample name:

Date: 19-10-2023 17:19:13

Number of reads: 1019891

Percentage reads mapped: 99.47

Strain: lineage4.4.1.1;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 0.52
lineage4 Euro-American LAM;T;S;X;H None 0.5
lineage4.4 Euro-American S;T None 0.54
lineage4.4.1 Euro-American (S-type) S;T None 0.55
lineage4.4.1.1 Euro-American S;Orphans None 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
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 1.0
gyrA 8056 p.Arg252Leu missense_variant 0.66
gyrA 9138 p.Gln613Glu missense_variant 0.6
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.39
rpoB 759746 c.-61C>T upstream_gene_variant 0.6
rpoC 762434 c.-936T>G upstream_gene_variant 0.27
rpoC 763031 c.-339T>C upstream_gene_variant 0.42
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.51
mmpL5 777416 c.1065G>T synonymous_variant 0.61
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.71
katG 2154724 p.Arg463Leu missense_variant 0.38
PPE35 2167926 p.Leu896Ser missense_variant 0.45
PPE35 2168479 p.Thr712Pro missense_variant 0.54
PPE35 2169840 p.Gly258Asp missense_variant 0.39
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.42
pncA 2289365 c.-125delC upstream_gene_variant 0.57
thyA 3074424 c.48G>T synonymous_variant 0.41
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.48
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 0.53
Rv3236c 3612665 p.Val151Ala missense_variant 0.27
embC 4242075 p.Arg738Gln missense_variant 0.66
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4328212 c.-740delC upstream_gene_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.69