TB-Profiler result

Run: ERR11465999
Summary

Run ID: ERR11465999

Sample name:

Date: 08-01-2024 01:57:16

Number of reads: 2883018

Percentage reads mapped: 99.47

Strain: lineage4.2.2.1;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 0.22
lineage4 Euro-American LAM;T;S;X;H None 0.75
lineage4.2 Euro-American H;T;LAM None 0.82
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.24
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.8
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.22
lineage4.2.2.1 Euro-American LAM7-TUR None 0.73
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 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.37
mshA 575907 p.Ala187Val missense_variant 0.16
mshA 576077 c.730C>T synonymous_variant 0.89
ccsA 620625 p.Ile245Met missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 0.31
rpoC 766500 p.Ala1044Val missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.23
mmpL5 776182 p.Asp767Asn missense_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833749 p.Ile70Leu missense_variant 0.2
rpsA 1834177 c.636A>C synonymous_variant 0.21
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102733 p.Leu104Phe missense_variant 0.34
katG 2154724 p.Arg463Leu missense_variant 0.27
PPE35 2167926 p.Leu896Ser missense_variant 0.21
Rv1979c 2222645 p.Leu174Phe missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714526 c.805_806delAC frameshift_variant 0.24
Rv2752c 3065711 p.Gly161Ser missense_variant 0.22
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.72
ald 3086742 c.-78A>C upstream_gene_variant 0.72
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 0.21
fbiB 3641640 p.Ala36Thr missense_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 0.28
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.12