Table 2 Quality control filtering result of SNPs.

From: Whole-genome sequencing identifies potential candidate genes for egg production traits in laying ducks (Anas platyrhynchos)

Name	ObsHET	PredHET	HWpval	%Geno	MAF	Rating
A1546176G	0.55	0.50	0.07	99.40	0.45
A1546196T	0.55	0.50	0.06	100.00	0.45
C1546217T	0.55	0.50	0.07	99.10	0.45
A1546400G	0.45	0.45	0.84	99.10	0.35
G1546616A	0.44	0.44	1.00	99.10	0.32
A1547351G	0.44	0.44	0.92	99.70	0.33
A1547887T	0.44	0.44	0.97	100.00	0.33
A1547889C	0.89	0.49	6.75 × 10^–59	100.00	0.45	BAD
C1548016T	0.55	0.50	0.07	99.40	0.45
C1548761T	0.44	0.44	1.00	99.40	0.32
G1550814A	0.32	0.38	4.10 × 10^–3	97.30	0.26
C1551010T	0.35	0.39	0.04	99.70	0.27
T1551159C	0.31	0.33	0.38	99.10	0.21
G1551821A	0.51	0.47	0.12	100.00	0.37
C1552291T	0.15	0.49	3.29 × 10^–36	93.90	0.43	BAD
A1552824T	0.34	0.45	4.86 × 10^–59	97.90	0.34	BAD
G1553772A	0.39	0.40	0.72	94.50	0.28
A1553775G	0.37	0.43	0.03	100.00	0.31
G1553886A	0.14	0.31	5.87 × 10^–20	99.40	0.19	BAD
C1553982G	0.31	0.33	0.37	99.40	0.21
T1554192C	0.37	0.43	0.02	99.40	0.31
A1554255G	0.16	0.33	5.38 × 10^–17	100.00	0.21	BAD
T1554298C	0.35	0.43	1.90 × 10^–3	97.30	0.31
T1557630C	0.26	0.42	2.12 × 10^–10	99.10	0.29	BAD
T1557633C	0.01	0.01	1.00	99.40	0.00	BAD
G1557719C	0.03	0.13	2.81 × 10^–19	98.80	0.07	BAD
C1557731G	0.07	0.08	0.03	98.20	0.04	BAD
C1557809T	0.03	0.10	5.35 × 10^–14	98.80	0.05	BAD
A1558367G	0.33	0.37	0.03	99.40	0.25
C1558458T	0.34	0.35	0.86	99.40	0.22
T1558531C	0.33	0.38	0.03	100.00	0.25
C1558820T	0.42	0.45	0.29	99.70	0.35
G1558943A	0.42	0.46	0.20	99.70	0.35
G1562443A	0.24	0.42	4.39 × 10^–13	93.30	0.30	BAD
A1562579G	0.38	0.37	0.62	99.70	0.24
G1562687C	0.21	0.36	7.01 × 10^–12	96.40	0.24	BAD
A1562993G	0.02	0.15	4.34 × 10^–29	99.10	0.08	BAD
G1564507A	0.42	0.44	0.50	93.90	0.33
C1565460T	0.75	0.47	9.46 × 10^–35	100.00	0.38	BAD
G1566061C	0.37	0.49	6.49 × 10^–6	98.80	0.43	BAD
C1566250T	0.36	0.40	0.11	96.40	0.27
C1567012T	0.43	0.43	1.00	100.00	0.31
G1567392C	0.51	0.47	0.30	100.00	0.39
A1567491G	0.40	0.44	0.16	97.60	0.32
T1570377C	0.43	0.43	0.97	99.40	0.31
C1570687T	0.43	0.45	0.40	100.00	0.35
A1570698G	0.40	0.45	0.07	97.30	0.35
A1571291G	0.34	0.35	0.70	100.00	0.22
A1571300G	0.05	0.34	8.68 × 10^–48	96.40	0.22	BAD
G1571845C	0.46	0.50	0.17	99.40	0.45
A1572228C	0.03	0.12	3.43 × 10^–17	98.50	0.06	BAD
A1572241G	0.21	0.50	1.94 × 10^–25	97.00	0.46	BAD
G1572493C	0.51	0.47	0.12	99.40	0.37

ObsHET the SNP's observed heterozygosity, PredHET the SNP's predicted heterozygosity, HWpval Hardy–Weinberg equilibrium P value, %Geno the percentage of non-missing genotypes for the SNPs, FamTrio the number of fully genotyped family trios for the SNPs, MendErr the number of observed Mendelian inheritance error, MAF minimum allele frequency.

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Table 2 Quality control filtering result of SNPs.

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