TB-Profiler result

Run: SRR4037661
Summary

Run ID: SRR4037661

Sample name:

Date: 21-10-2023 12:12:30

Number of reads: 4218756

Percentage reads mapped: 99.52

Strain: lineage4.4.1.1;lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.14
lineage4 Euro-American LAM;T;S;X;H None 0.87
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.12
lineage4.4 Euro-American S;T None 0.86
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.16
lineage4.4.1 Euro-American (S-type) S;T None 0.86
lineage4.4.1.1 Euro-American S;Orphans None 0.85
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 9138 p.Gln613Glu missense_variant 0.88
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 0.19
rpoC 763031 c.-339T>C upstream_gene_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.16
mmpL5 777416 c.1065G>T synonymous_variant 0.88
mmpS5 779615 c.-710C>G upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673363 c.-839G>A upstream_gene_variant 0.82
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.86
PPE35 2167926 p.Leu896Ser missense_variant 0.14
PPE35 2168479 p.Thr712Pro missense_variant 0.87
PPE35 2169840 p.Gly258Asp missense_variant 0.88
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066175 p.Pro6Arg missense_variant 0.76
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.8
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 0.93
Rv3236c 3612665 p.Val151Ala missense_variant 0.92
Rv3236c 3612813 p.Thr102Ala missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.12
gid 4407620 p.Tyr195His missense_variant 0.12
gid 4407927 p.Glu92Asp missense_variant 0.14