TB-Profiler result

Run: ERR245754
Summary

Run ID: ERR245754

Sample name:

Date: 20-10-2023 19:09:58

Number of reads: 12932897

Percentage reads mapped: 99.41

Strain: lineage4.1.2;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 0.43
lineage4 Euro-American LAM;T;S;X;H None 0.57
lineage4.1 Euro-American T;X;H None 0.57
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.44
lineage4.1.2 Euro-American T;H None 0.57
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.43
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 7323 p.Pro8Ala missense_variant 0.53
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.57
fgd1 491742 c.960T>C synonymous_variant 0.42
mshA 575907 p.Ala187Val missense_variant 0.47
ccsA 620625 p.Ile245Met missense_variant 0.43
rpoB 760115 c.309C>T synonymous_variant 0.54
rpoC 763031 c.-339T>C upstream_gene_variant 0.4
rpoC 765150 p.Gly594Glu missense_variant 0.55
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.41
mmpL5 776182 p.Asp767Asn missense_variant 0.42
mmpL5 776659 p.Asp608Asn missense_variant 0.55
mmpS5 779615 c.-710C>G upstream_gene_variant 0.42
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.38
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103226 c.-184C>G upstream_gene_variant 0.43
katG 2154724 p.Arg463Leu missense_variant 0.44
PPE35 2167926 p.Leu896Ser missense_variant 0.41
PPE35 2168501 p.Phe704Leu missense_variant 0.52
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.58
ald 3086739 c.-81G>A upstream_gene_variant 0.42
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.35
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embC 4242803 p.Val981Leu missense_variant 0.55
embA 4243460 c.228C>T synonymous_variant 0.4
embB 4247121 p.Ser203Leu missense_variant 0.61
aftB 4267647 p.Asp397Gly missense_variant 0.37
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.38
gid 4407927 p.Glu92Asp missense_variant 0.43