TB-Profiler result

Run: SRR6824299
Summary

Run ID: SRR6824299

Sample name:

Date: 20-10-2023 19:35:20

Number of reads: 17335192

Percentage reads mapped: 98.33

Strain: lineage4.5;lineage2.2.1

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (0.22)
Isoniazid R katG p.Ser315Thr (0.25)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.21)
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 0.21
lineage4 Euro-American LAM;T;S;X;H None 0.81
lineage4.5 Euro-American H;T RD122 0.8
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.21
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.2
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
rpoB 761155 p.Ser450Leu missense_variant 0.22 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.21 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.25 isoniazid
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 7892 c.591G>A synonymous_variant 0.79
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.21
mshA 575907 p.Ala187Val missense_variant 0.2
ccsA 620029 c.139C>T synonymous_variant 0.78
ccsA 620625 p.Ile245Met missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 0.21
rpoC 764817 p.Val483Gly missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.21
mmpL5 776182 p.Asp767Asn missense_variant 0.19
mmpR5 779079 p.Arg30Ser missense_variant 0.81
mmpS5 779615 c.-710C>G upstream_gene_variant 0.19
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302905 c.-26T>G upstream_gene_variant 0.21
Rv1258c 1406101 p.Pro414Ser missense_variant 0.78
Rv1258c 1406760 c.580_581insC frameshift_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476077 n.2420T>G non_coding_transcript_exon_variant 0.81
fabG1 1673359 c.-81T>G upstream_gene_variant 0.81
inhA 1674210 c.9A>C synonymous_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.23
PPE35 2167926 p.Leu896Ser missense_variant 0.18
PPE35 2170568 p.Ile15Met missense_variant 0.83
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.22
alr 3841207 p.His72Tyr missense_variant 0.19
rpoA 3877482 c.1026C>T synonymous_variant 0.78
rpoA 3878575 c.-68C>T upstream_gene_variant 0.87
clpC1 4038318 p.Pro796Leu missense_variant 0.8
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.21
embB 4247828 p.Ala439Thr missense_variant 0.82
aftB 4267647 p.Asp397Gly missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.15
gid 4407927 p.Glu92Asp missense_variant 0.16