3.1 Ploidy identification and variant calling
Whole genome resequencing of the 151 individuals generated a total of
~ 10.6 G of clean paired-end reads (70.2 M per
individual), giving an average sequencing depth of 12.2× (Table S1).
Among them, 99.14% of reads were on average mapped to the reference
genome of goldfish. The analysis of allele frequency distributions at
biallelic variants clearly showed one Gaussian distribution with mean
0.5 for diploids and bimodal distributions with means 0.33 and 0.67 for
triploid (Figure S1). Among all individuals, 73 and 78 were identified
as diploids and triploids, respectively. In invasive populations, the
number of diploids and triploids were 29 and 9 in the LL population, and
2 and 22 in the CBL population, respectively (Table 1). In direct source
regions, samples from Ningxia and Sichuan were almost all triploids with
only one diploid detected from Sichuan. In indirect source regions, 29
diploids and 6 triploids were detected. After variant calling and
filtering, a total of 16,888,283 and 17,954,020 SNPs were identified
from diploids and triploids, respectively, with 10,719,815 SNPs being
common to both ploidy categories.