Table 1 Sequencing and alignment statistics.

Sample (pool)	Reads^a	Cannabis var. Finola reference			Cannabis var. Purple Kush reference
Sample (pool)	Reads^a	Reads aligned^b	Depth of coverage^c	Breadth of coverage (%)^d	Reads aligned^b	Depth of coverage^c	Breadth of coverage (%)^d
CBDA	501,992,266	497,228,282	53.76	75.00	494,924,047	66.11	79.21
THCVA	477,836,956	473,117,256	52.65	72.05	471,191,752	63.19	78.64

Haploid genome length for concatenated Cannabis sativa L. var. Finola reference [GenBank: ASM341772v2] is 1,010,967,789 bp; haploid genome length for the concatenated Cannabis sativa L. var. Purple Kush reference [GenBank: ASM23057v2] is 900,956,908 bp; reference scaffolds concatenated into separate supper scaffolds using ScaffoldStitcher (see “Methods”); CBDA: cannabidiolic acid; THCVA: tetrahydrocannabivarinic acid.
^aTotal number of reads including the first and second read of pairs; reads sequenced according to the 2 × 125 bp (550 bp insert) paired end (PE) scheme.
^bTotal number of reads including the first and second read of pairs passing Illumina’s filter that aligned to the reference sequence.
^cMean sequencing depth (mean number of mapped reads that cover each base of the reference sequence).
^dPercentage of bases of the reference sequence covered with mapped reads at a sequencing depth ≥ 15 ×.

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