Table 2. Open in new tab One-population... | Oxford Academic

Table 2.

Open in new tab

One-population YRI model analysis results.

			Depth
Parameter	AFS	Model	$30 \times$	$10 \times$	$5 \times$	$3 \times$
$ν_{YRI}$	GATK	dadi	1.82	1.76	1.55	0.05
	GATK	Low-pass	1.83	1.79	1.74	1.57
	ANGSD	dadi	1.82	1.83	1.71	0.08
	winsfs	dadi	1.80	1.84	1.72	0.08
T	GATK	dadi	0.43	0.51	0.91	0.001
	GATK	Low-pass	0.43	0.47	0.47	0.44
	ANGSD	dadi	0.60	0.73	1.02	0.001
	winsfs	dadi	0.55	0.74	1.03	0.001
θ $(\times 10^{4})$	GATK	dadi	5.14	5.07	4.77	5.99
	GATK	Low-pass	5.15	5.11	5.12	5.16
	ANGSD	dadi	5.48	5.24	4.93	6.80
	winsfs	dadi	5.52	5.21	4.90	6.81
Log-likelihood	GATK	dadi	$-$ 289	$-$ 258	$-$ 557	$-$ 1,301
	GATK	Low-pass	$-$ 294	$-$ 289	$-$ 327	$-$ 347
	ANGSD	dadi	$-$ 467	$-$ 495	$-$ 1,188	$-$ 5,674
	winsfs	dadi	$-$ 497	$-$ 584	$-$ 1,207	$-$ 3,443

			Depth
Parameter	AFS	Model	$30 \times$	$10 \times$	$5 \times$	$3 \times$
$ν_{YRI}$	GATK	dadi	1.82	1.76	1.55	0.05
	GATK	Low-pass	1.83	1.79	1.74	1.57
	ANGSD	dadi	1.82	1.83	1.71	0.08
	winsfs	dadi	1.80	1.84	1.72	0.08
T	GATK	dadi	0.43	0.51	0.91	0.001
	GATK	Low-pass	0.43	0.47	0.47	0.44
	ANGSD	dadi	0.60	0.73	1.02	0.001
	winsfs	dadi	0.55	0.74	1.03	0.001
θ $(\times 10^{4})$	GATK	dadi	5.14	5.07	4.77	5.99
	GATK	Low-pass	5.15	5.11	5.12	5.16
	ANGSD	dadi	5.48	5.24	4.93	6.80
	winsfs	dadi	5.52	5.21	4.90	6.81
Log-likelihood	GATK	dadi	$-$ 289	$-$ 258	$-$ 557	$-$ 1,301
	GATK	Low-pass	$-$ 294	$-$ 289	$-$ 327	$-$ 347
	ANGSD	dadi	$-$ 467	$-$ 495	$-$ 1,188	$-$ 5,674
	winsfs	dadi	$-$ 497	$-$ 584	$-$ 1,207	$-$ 3,443

Inferred demographic parameters in dadi using empirical GATK and ANGSD AFS. We analyzed GATK empirical spectra without (dadi) and with low-pass correction (low-pass).

Table 2.

Open in new tab

One-population YRI model analysis results.

			Depth
Parameter	AFS	Model	$30 \times$	$10 \times$	$5 \times$	$3 \times$
$ν_{YRI}$	GATK	dadi	1.82	1.76	1.55	0.05
	GATK	Low-pass	1.83	1.79	1.74	1.57
	ANGSD	dadi	1.82	1.83	1.71	0.08
	winsfs	dadi	1.80	1.84	1.72	0.08
T	GATK	dadi	0.43	0.51	0.91	0.001
	GATK	Low-pass	0.43	0.47	0.47	0.44
	ANGSD	dadi	0.60	0.73	1.02	0.001
	winsfs	dadi	0.55	0.74	1.03	0.001
θ $(\times 10^{4})$	GATK	dadi	5.14	5.07	4.77	5.99
	GATK	Low-pass	5.15	5.11	5.12	5.16
	ANGSD	dadi	5.48	5.24	4.93	6.80
	winsfs	dadi	5.52	5.21	4.90	6.81
Log-likelihood	GATK	dadi	$-$ 289	$-$ 258	$-$ 557	$-$ 1,301
	GATK	Low-pass	$-$ 294	$-$ 289	$-$ 327	$-$ 347
	ANGSD	dadi	$-$ 467	$-$ 495	$-$ 1,188	$-$ 5,674
	winsfs	dadi	$-$ 497	$-$ 584	$-$ 1,207	$-$ 3,443

			Depth
Parameter	AFS	Model	$30 \times$	$10 \times$	$5 \times$	$3 \times$
$ν_{YRI}$	GATK	dadi	1.82	1.76	1.55	0.05
	GATK	Low-pass	1.83	1.79	1.74	1.57
	ANGSD	dadi	1.82	1.83	1.71	0.08
	winsfs	dadi	1.80	1.84	1.72	0.08
T	GATK	dadi	0.43	0.51	0.91	0.001
	GATK	Low-pass	0.43	0.47	0.47	0.44
	ANGSD	dadi	0.60	0.73	1.02	0.001
	winsfs	dadi	0.55	0.74	1.03	0.001
θ $(\times 10^{4})$	GATK	dadi	5.14	5.07	4.77	5.99
	GATK	Low-pass	5.15	5.11	5.12	5.16
	ANGSD	dadi	5.48	5.24	4.93	6.80
	winsfs	dadi	5.52	5.21	4.90	6.81
Log-likelihood	GATK	dadi	$-$ 289	$-$ 258	$-$ 557	$-$ 1,301
	GATK	Low-pass	$-$ 294	$-$ 289	$-$ 327	$-$ 347
	ANGSD	dadi	$-$ 467	$-$ 495	$-$ 1,188	$-$ 5,674
	winsfs	dadi	$-$ 497	$-$ 584	$-$ 1,207	$-$ 3,443

Inferred demographic parameters in dadi using empirical GATK and ANGSD AFS. We analyzed GATK empirical spectra without (dadi) and with low-pass correction (low-pass).