TB-Profiler result

Run: SRR6650257
Summary

Run ID: SRR6650257

Sample name:

Date: 15-08-2023 07:39:35

Number of reads: 3670153

Percentage reads mapped: 99.57

Strain: lineage2.2.1.1

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 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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576150 p.Val268Gly missense_variant 0.21
mshA 576735 p.Leu463Arg missense_variant 0.19
mshA 576744 p.Val466Gly missense_variant 0.26
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.31
ccsA 620756 p.Asp289Gly missense_variant 0.28
rpoB 759620 c.-187A>C upstream_gene_variant 0.23
rpoB 759706 c.-101T>C upstream_gene_variant 0.26
rpoB 759776 c.-31T>G upstream_gene_variant 0.21
rpoB 759784 c.-23A>C upstream_gene_variant 0.17
rpoB 759785 c.-22T>G upstream_gene_variant 0.12
rpoB 762924 p.Thr1040Pro missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.94
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777427 p.Thr352Pro missense_variant 0.26
mmpR5 779339 p.Leu117Arg missense_variant 0.21
mmpR5 779348 p.Val120Gly missense_variant 0.25
mmpR5 779354 p.Leu122Arg missense_variant 0.25
mmpR5 779369 p.Asp127Ala missense_variant 0.35
mmpR5 779371 p.Ala128Pro missense_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.32
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474500 n.843T>G non_coding_transcript_exon_variant 0.29
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155856 p.Thr86Pro missense_variant 0.33
PPE35 2167660 p.Thr985Pro missense_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.12
PPE35 2170053 p.Thr187Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289874 c.-633C>T upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.39
ahpC 2726341 p.Val50Gly missense_variant 0.31
pepQ 2859904 p.Val172Gly missense_variant 0.28
Rv2752c 3064745 p.Thr483Pro missense_variant 0.24
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339749 p.Val211Gly missense_variant 0.26
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642751 p.Asp406Ala missense_variant 0.23
ddn 3986997 p.Thr52Pro missense_variant 0.23
embC 4242390 p.Leu843Arg missense_variant 0.19
embA 4242406 c.-827A>C upstream_gene_variant 0.22
embC 4242422 p.Trp854Gly missense_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.36
embA 4243216 c.-17G>A upstream_gene_variant 0.97
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248115 c.1602C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethR 4327637 p.Leu30Pro missense_variant 0.25
ethR 4327652 p.Asn35Thr missense_variant 0.27
ethR 4327664 p.Asp39Ala missense_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0