TB-Profiler result

Run: SRR6824680
Summary

Run ID: SRR6824680

Sample name:

Date: 20-10-2023 19:32:43

Number of reads: 9040066

Percentage reads mapped: 99.09

Strain: lineage2.2.1

Drug-resistance: RR-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 (1.00)
Isoniazid
Ethambutol
Pyrazinamide R pncA p.Val139Leu (0.40), pncA p.Thr76Pro (0.19), pncA p.Thr47Ala (0.24)
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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
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 1.0 rifampicin
pncA 2288827 p.Val139Leu missense_variant 0.4 pyrazinamide
pncA 2289016 p.Thr76Pro missense_variant 0.19 pyrazinamide
pncA 2289103 p.Thr47Ala missense_variant 0.24 pyrazinamide
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 5261 p.Ala8Thr missense_variant 1.0
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 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765612 p.His748Pro missense_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.11
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.1
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.1
rrs 1473097 n.1252G>A non_coding_transcript_exon_variant 0.13
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.13
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.13
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.13
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.14
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.14
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.14
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.14
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13
rrs 1473147 n.1302G>A non_coding_transcript_exon_variant 0.12
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.11
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.11
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.12
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.11
rpsA 1833410 c.-132G>A upstream_gene_variant 0.99
rpsA 1834177 c.636A>C synonymous_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
katG 2155708 p.Trp135Ser missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168940 p.Leu558Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
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 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247574 p.Asp354Gly missense_variant 0.99
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.99