TB-Profiler result

Run: SRR2101090
Summary

Run ID: SRR2101090

Sample name:

Date: 19-10-2023 17:02:40

Number of reads: 5045306

Percentage reads mapped: 99.53

Strain: lineage4.9;lineage2.2.1;lineage1

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 0.78
lineage4 Euro-American LAM;T;S;X;H None 0.07
lineage1 Indo-Oceanic EAI RD239 0.12
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.82
lineage4.9 Euro-American (H37Rv-like) T1 None 0.09
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.81
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
gyrB 6112 p.Met291Ile missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.87
gyrA 8452 p.Ala384Val missense_variant 0.16
gyrA 9143 c.1842T>C synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 0.91
fgd1 491742 c.960T>C synonymous_variant 0.94
mshA 575907 p.Ala187Val missense_variant 0.88
ccsA 620625 p.Ile245Met missense_variant 0.82
rpoC 763031 c.-339T>C upstream_gene_variant 0.89
mmpL5 775639 p.Ile948Val missense_variant 0.89
mmpL5 776100 p.Thr794Ile missense_variant 0.92
mmpL5 776182 p.Asp767Asn missense_variant 0.8
mmpS5 779615 c.-710C>G upstream_gene_variant 0.76
rpsL 781395 c.-165T>C upstream_gene_variant 0.93
Rv1258c 1406760 c.580_581insC frameshift_variant 0.83
embR 1417019 p.Cys110Tyr missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.81
tlyA 1917972 c.33A>G synonymous_variant 0.99
katG 2154724 p.Arg463Leu missense_variant 0.94
PPE35 2167926 p.Leu896Ser missense_variant 0.92
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.92
eis 2714526 c.805_806delAC frameshift_variant 0.78
ahpC 2726051 c.-142G>A upstream_gene_variant 0.16
Rv2752c 3065711 p.Gly161Ser missense_variant 0.82
ald 3086788 c.-32T>C upstream_gene_variant 0.94
Rv3083 3448714 p.Asp71His missense_variant 0.26
Rv3083 3449836 p.Lys445Gln missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.91
fprA 3474597 c.591C>A synonymous_variant 0.16
fprA 3475159 p.Asn385Asp missense_variant 0.16
Rv3236c 3612813 p.Thr102Ala missense_variant 0.84
clpC1 4040517 p.Val63Ala missense_variant 0.11
embC 4240671 p.Thr270Ile missense_variant 0.21
embC 4241042 p.Asn394Asp missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 0.84
embA 4243460 c.228C>T synonymous_variant 0.72
embA 4245969 p.Pro913Ser missense_variant 0.16
embB 4247646 p.Glu378Ala missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 0.84
aftB 4269606 c.-770T>C upstream_gene_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.22
gid 4407588 c.615A>G synonymous_variant 0.92
gid 4407927 p.Glu92Asp missense_variant 0.86