Table 2 Number of short variants called using extreme-phenotype bulk pools when mapped to Finola and Purple Kush Cannabis reference sequences.

From: An extreme-phenotype genome‐wide association study identifies candidate cannabinoid pathway genes in Cannabis

Reference

Variant

Rawc

Filteredd

Cannabis sativa L. var. Finolaa

SNP

19,500,079

9,133,504

 

InDel

5,785,376

2,593,786

 

TOTAL (SNP + InDel)

25,285,455

11,727,290

Cannabis sativa L. var. Purple Kushb

SNP

17,483,802

7,926,104

 

InDel

5,876,231

2,714,230

 

TOTAL (SNP + InDel)

23,360,033

10,640,334

  1. SNP single nucleotide polymorphism, InDel small insertion-deletion.
  2. aConcatenated Cannabis sativa L. var. Finola reference sequence [GenBank: ASM341772v2].
  3. bConcatenated Cannabis sativa L. var. Purple Kush reference sequence [GenBank: ASM23057v2].
  4. cRaw unfiltered variants called using GATK HaplotypeCaller.
  5. dHard filtered biallelic variants with depth of coverage (DP) ≥ 15 × and genotype quality (GQ) ≥ 20 that had genotype calls for both chemotypic pools at the variant site.
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