TB-Profiler result

Run: SRR23862086
Summary

Run ID: SRR23862086

Sample name:

Date: 12-04-2023 17:59:05

Number of reads: 4427156

Percentage reads mapped: 99.69

Strain: lineage4.8;lineage2.2.1

Drug-resistance: Other

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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 R gid c.102delG (0.90)
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 0.16
lineage4 Euro-American LAM;T;S;X;H None 0.84
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.15
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.86
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.15
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
gid 4408100 c.102delG frameshift_variant 0.9 streptomycin
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
fgd1 491742 c.960T>C synonymous_variant 0.14
ccsA 620625 p.Ile245Met missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 0.12
rpoC 766645 p.Glu1092Asp missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.12
mmpL5 776182 p.Asp767Asn missense_variant 0.14
mmpL5 777883 p.Gly200Arg missense_variant 0.16
mmpS5 779615 c.-710C>G upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.75
fabG1 1673553 p.Asp38Glu missense_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 0.13
PPE35 2168149 p.Pro822Ser missense_variant 0.93
PPE35 2170065 p.Ala183Gly missense_variant 0.19
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.16
pepQ 2860159 p.Ala87Gly missense_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 0.18
ald 3087816 p.Cys333Gly missense_variant 0.13
fbiD 3339734 p.Ala206Gly missense_variant 0.73
fbiD 3339751 p.Ala212Pro missense_variant 0.26
Rv3083 3448322 c.-182G>A upstream_gene_variant 0.88
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 0.18
rpoA 3878641 c.-134C>G upstream_gene_variant 0.42
embC 4240409 p.Pro183Ala missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.15
embB 4246584 p.Arg24Pro missense_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.15