Trios-based inquiry into de novo copy number variants in the swine genome

Magdalena Frąszczak; Błażej Nowak; Martyna Kaźmierczak; Magda Mielczarek

doi:10.2478/aoas-2025-0120

Trios-based inquiry into de novo copy number variants in the swine genome

Annals of Animal Science

AHEAD OF PRINT

By: Magdalena Frąszczak, Błażej Nowak, Martyna Kaźmierczak and Magda Mielczarek

Open Access

|Feb 2026

Figures & Tables

The whole genome sequencing experimental design. A black arrow indicates the paternal contribution, while a red/blue arrow indicates the maternal. S corresponds to sire, D to dam, and O to offspring. Family 1 is represented by red, while Family 2 is represented by blue

The similarity between animals in overlapping deletions. S corresponds to sire, D to dam, and O to offspring. Family 1 is represented by red, while Family 2 is represented by blue

The similarity between animals in overlapping duplications. S corresponds to sire, D to dam, and O to offspring. Family 1 is represented by red, while Family 2 is represented by blue

Copy number variant (CNV) overlap within families. The left black column shows the number of CNV regions (CNVRs) detected in all animals. The green/navy blue/blue/navy red columns give the number of CNVRs found in five/four/three/two animals, and the dots below the columns denote the animals with these variants. The red columns correspond to CNVs unique to each individual. The first three red columns always correspond to the number of *de novo* CNVRs present in offspring. The horizontal columns are the total CNVRs identified in each animal. The first two graphs (a and b) show deletion regions, and the latter (c and d) refer to duplication regions

The frequency of *de novo* copy number variants (CNVs) to all CNVs

Genomic distribution of *de novo* deletions identified in the six offspring

Genomic distribution of *de novo* duplications identified in the six offspring

Additional files
Sample name	Sample ID	% of mapped reads	% of properly mapped reads	Average genome coverage after alignment
Family 1
Sire 1	S1	98.42	95.36	13
Dam 1	D1	98.53	96	11
Dam 2	D2	98.11	95.37	15
Offspring 1	O1_S1D1	98.41	95.58	16
Offspring 2	O2_S1D1	98.36	95.36	15
Offspring 3	O3_S1D2	98.3	95.31	14
Family 2
Sire 2	S2	98.48	95.47	10
Dam 3	D3	98.6	95.82	12
Dam 4	D4	98.57	95.8	19
Offspring 4	O4_S2D3	98.42	95.54	12
Offspring 5	O5_S2D3	98.55	95.53	12
Offspring 6	O6_S2D4	98.37	95.42	18

[i] Additional file 1. A summary of basic alignment statistics, including the percentage of aligned reads and properly paired reads, as well as the average genome coverage after alignment.

Number of deletions identified in each animal.

Number of duplications identified in each animal.

chr	chr length	cnv counts	cnv length	coverage (%)	max size	mean length	min size
deletions
1	274330532	560	824000	0.300	41000	3951.07	600
2	151935994	667	1141400	0.751	70000	7324.74	600
3	132848913	238	404000	0.304	57200	4168.07	600
4	130910915	344	638400	0.488	114600	10021.51	600
5	104526007	364	478200	0.457	34200	4053.30	600
6	170843587	387	1076600	0.630	119600	8284.24	600
7	121844099	466	668200	0.548	99600	6597.85	600
8	138966237	355	667200	0.48	56400	6371.27	600
9	139512083	478	1343600	0.963	183400	8183.26	600
10	69359453	157	271800	0.392	65000	3526.11	600
11	79169978	340	449600	0.568	59200	5214.12	600
12	61602749	233	547200	0.888	195000	11570.82	600
13	208334590	481	1159200	0.556	140200	9968.40	600
14	141755446	423	718600	0.507	100200	6244.44	600
15	140412725	377	609400	0.434	53000	5449.87	600
16	79944280	262	329400	0.412	53400	3223.66	600
17	63494081	248	417600	0.658	189600	6933.06	600
18	55982971	49	131800	0.235	44800	5779.59	600

chr	chr length	cnv counts	cnv length	coverage (%)	max size	mean length	min size
duplications
1	274330532	510	1423600	0.519	163600	13505.88	2200
2	151935994	482	1779800	1.171	174200	23009.96	1400
3	132848913	138	421400	0.317	52000	15779.71	2000
4	130910915	217	694400	0.530	193800	16544.70	1200
5	104526007	367	1103400	1.056	217200	20102.45	2600
6	170843587	144	582200	0.341	80200	17461.11	2800
7	121844099	629	2127800	1.746	198400	19948.17	2000
8	138966237	125	1001800	0.721	561400	64956.8	2000
9	139512083	333	1355600	0.972	239000	22518.32	1800
10	69359453	49	129600	0.187	27400	14934.69	2800
11	79169978	189	494400	0.624	69600	11987.30	2200
12	61602749	190	538600	0.874	49400	16998.95	1600
13	208334590	163	713000	0.342	157600	30195.09	2000
14	141755446	279	732600	0.517	54000	13179.93	2200
15	140412725	70	382400	0.272	91400	25354.29	2000
16	79944280	32	199800	0.250	52800	13981.25	2800
17	63494081	196	633600	0.998	117200	18442.86	1600
18	55982971	11	92200	0.165	54200	11054.55	4600

[i] Additional file 4. Basic statistics for length and counts of all copy number variants (CNVs), depending on the chromosome.

chr	chr length	cnv counts	cnv length	coverage (%)	max size	mean length	min size
de novo deletions
1	274330532	55	222000	0.081	36000	4036.36	600
2	151935994	34	186000	0.122	70000	5470.58	600
3	132848913	33	74600	0.056	13400	2260.60	600
4	130910915	23	63400	0.048	11800	2756.52	600
5	104526007	22	79400	0.075	24600	3609.09	600
6	170843587	30	97200	0.056	17600	3240.00	600
7	121844099	24	60800	0.049	11000	2533.33	600
8	138966237	16	71000	0.051	36400	4437.50	600
9	139512083	31	179600	0.128	41000	5793.54	600
10	69359453	11	18400	0.026	3800	1672.72	600
11	79169978	13	37200	0.046	9200	2861.53	600
12	61602749	12	16800	0.027	4200	1400.00	600
13	208334590	33	117800	0.056	28200	3569.69	600
14	141755446	27	61600	0.043	12400	2281.48	600
15	140412725	18	78800	0.056	29000	4377.77	600
16	79944280	18	38600	0.048	10200	2144.44	600
17	63494081	14	61600	0.097	28000	4400.00	600
18	55982971	8	23200	0.041	13000	2900.00	600

chr	chr length	cnv counts	cnv length	coverage (%)	max size	mean length	min size
de novo duplications
1	274330532	17	233200	0.085	39200	13717.65	2200
2	151935994	14	118400	0.078	27800	8457.14	1400
3	132848913	2	10800	0.008	6200	5400.00	4600
4	130910915	4	48200	0.037	33800	12050.00	3000
5	104526007	1	14800	0.014	14800	14800.00	14800
6	170843587	5	55600	0.033	29000	11120.00	3200
7	121844099	12	193800	0.159	70000	16150.00	3200
8	138966237	6	52000	0.037	15000	8666.67	3800
9	139512083	8	60800	0.044	16400	7600.00	4400
10	69359453	2	31000	0.045	17600	15500.00	13400
11	79169978	4	40400	0.051	14000	10100.00	5000
12	61602749	2	19200	0.031	11400	9600.00	7800
13	208334590	5	47400	0.023	15600	9480.00	5400
14	141755446	3	26200	0.018	16000	8733.33	4000
15	140412725	4	31600	0.023	11600	7900.00	3200
16	79944280	3	43000	0.054	19600	14333.33	10000
17	63494081	2	40400	0.064	32200	20200.00	8200
18	55982971	2	14600	0.026	8800	7300.00	5800

[i] Additional file 5. Basic statistics for length and counts of de novo copy number variants (CNVs), depending on the chromosome.

	O1_S1D1	O2_S1D1	O3_S1D2	O4_S2D3	O5_S2D3	O6_S2D4
P -value	3.76⋅10⁻⁵	1.26⋅10⁻⁶	6.49⋅10⁻⁷	0.13⋅10⁻¹	0.17⋅10⁻³	8.18⋅10⁻⁷

[i] Additional file 6. Mann-Whitney U test showing that de novo deletions are shorter than inherited.

min	1st qu.	median	mean	3rd qu	max	sd	number
de novo deletions
600	800	1400	2835	2850	23000	3890.368	80
600	800	1400	3472.5	3450	36000	5684.466	80
600	800	2600	3935.714	4050	36400	5695.179	56
600	800	1200	4515.556	3800	29000	7038.012	45
600	800	1600	2972.549	3000	28000	4424.662	51
600	800	1800	3710.909	2800	70000	7991.858	110
inherited deletions
600	1800	4200	11637.64	9600	194600	23621.46	457
600	1600	3800	11657.99	9550	195000	25709.8	438
600	1800	4200	10456.46	9600	187800	18723.54	379
600	2000	4400	10830.46	9200	195000	22087.34	394
600	2200	4600	12348.79	11350	194600	24186.72	414
600	1600	3500	10816.85	8600	195000	24060.52	534
de novo duplications
1800	5200	7600	13147.83	17100	44200	12181.09	23
3200	7000	8200	11711.11	13900	39200	7987.169	27
5400	7150	10500	10866.67	14000	17600	4865.662	6
5400	8200	8800	8800	9850	11600	2097.618	6
2600	4900	7800	8200	10600	16400	4170.224	14
1400	3500	6400	11500	12750	70000	15423.77	20
inherited duplications
2200	12000	23600	41910.22	50400	563200	57319.37	225
2200	12000	23200	42234.06	49600	563200	60354.32	229
1200	13700	26000	46173.26	54500	563200	63677.16	187
2200	13800	27000	46524.85	55400	563200	63077.09	165
1200	13850	26200	47055.17	53300	563200	65834.85	174
2200	11600	23000	39696.85	44950	563200	56621.46	254

[i] Additional file 7. Basic statistics for the length of de novo and inherited copy number variants (CNVs) in offspring.

Gene-level overlap between the *de novo* copy number variants (CNVs). (a) Visualisation of the ENSSSCG00000017645 (*TEX14*; chr12:34815476–34912766). Two CNVs (my_data_2) were identified within the gene boundaries: chr12:34888201-34899600 (duplication), chr12:34899601-34900400 (deletion). (b) Visualisation of the ENSSSCG00000004032 gene location (*PRKN*; chr1:5465312–6730872). Three CNVs (my_data_1) were identified within the gene boundaries: chr1:5514201-5516400 (duplication_1), chr1:5908601-5911400 (deletion), chr1:6264201-6273000 (duplication_2).

Gene ontologies (GOs) with fold enrichment and the number of genes corresponding to the GO term. The false discovery rate (FDR) reflects the statistical significance of the enrichment (adjusted p-values for multiple testing to control the proportion of type I errors). Fold Enrichment measures the enrichment magnitude. Higher values indicate stronger enrichment and are an important metric of effect size. N. of Genes is the number of genes in the ontology that overlap with a gene list provided by a user.

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DOI: https://doi.org/10.2478/aoas-2025-0120 | Journal eISSN: 2300-8733 (formerly 1642-3402) | Journal ISSN: 1642-3402

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Language: English

Submitted on: Feb 18, 2025

Accepted on: Oct 14, 2025

Published on: Feb 16, 2026

Published by: National Research Institute of Animal Production

In partnership with: Paradigm Publishing Services

Publication frequency: 4 issues per year

Keywords:

copy number variants,

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© 2026 Magdalena Frąszczak, Błażej Nowak, Martyna Kaźmierczak, Magda Mielczarek, published by National Research Institute of Animal Production
This work is licensed under the Creative Commons Attribution 3.0 License.

AHEAD OF PRINT

Trios-based inquiry into de novo copy number variants in the swine genome

Figures & Tables

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

Figure 7.

Additional file 2.

Additional file 3.

Additional file 8.

Additional file 9.

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