Accumulation of genetic variants associated with immunity in the selective breeding of broilers

Zou, Angela; Nadeau, Kerry; Wang, Pauline W.; Lee, Jee Yeon; Guttman, David S.; Sharif, Shayan; Korver, Doug R.; Brumell, John H.; Parkinson, John

doi:10.1186/s12863-020-0807-z

BMC Genomic Data

Table 1 Sequencing and genomic variant statistics for breeds used in this study

From: Accumulation of genetic variants associated with immunity in the selective breeding of broilers

	Sequencing Statistics						Summary of SNPs Identified By Feature and Impact
	Sequencing Method	Total # of reads	Aligned Reads	Unmapped	Breadth of coverage	Average read depth	Synonymous	Non-synonymous	Intergenic	Intronic	UTR5	UTR3	Frameshift indel	Non-frameshift indel	Stop gain	Stop loss
1957	NextSeq	954,402,120	771,590,591	178,041,952	90%	89	63,573	28,697	2,733,442	3,917,443	50,831	139,826	2993	973	203	38
1978	NextSeq	956,913,758	813,956,611	124,470,402	90%	91	70,413	31,930	2,953,408	4,317,698	57,084	151,967	3145	1013	225	50
Ross 308	NextSeq	753,170,974	688,175,109	20,392,933	90%	83	70,208	31,791	2,933,982	4,283,304	56,713	152,151	3030	1006	245	47
Silkie	Illumina GAII	250,344,910	183,908,065	4,059,840	91%	16	18,035	5120	5,769,436	1,141,875	2571	25,457	191	111	11	2
L2	Illumina GAII	319,254,874	226,413,441	4,765,903	93%	19	18,131	5206	5,804,968	1,141,600	2829	25,680	226	121	14	2
CB1	SOLiD	302,271,430	191,347,790	99,593,871	90%	8	8444	2085	2,009,820	404,234	646	9286	136	121	6	1
CB2	SOLiD	225,049,549	138,854,319	78,806,791	89%	3	4945	1171	1,270,404	262,783	329	5916	73	63	3	0
High	SOLiD	285,510,087	186,711,973	89,131,046	86%	4	3874	1005	1,058,205	218,944	245	4974	67	64	1	0
Low	SOLiD	311,562,452	201,484,147	98,719,567	88%	4	2419	630	706,923	146,740	173	3255	22	18	1	0
Obese	SOLiD	214,645,321	127,085,837	80,434,294	89%	6	5203	1313	1,309,898	267,762	395	5958	80	71	3	0
RIR	SOLiD	182,411,411	111,322,051	64,677,509	89%	5	3996	989	972,200	196,322	257	4490	46	40	1	2
WLA	SOLiD	311,017,596	176,885,293	101,265,637	91%	7	7334	1959	1,972,780	406,528	650	9128	143	130	4	1
WLB	SOLiD	179,401,459	132,406,702	39,517,064	88%	5	5640	1465	1,562,666	319,525	396	7104	93	86	1	0
RJF	SOLiD	176,071,566	112,046,668	57,045,807	88%	5	309	80	66,657	12,527	14	324	18	15	0	0
RJFswe	SOLiD	355,473,025	254,348,419	131,460,569	91%	10	10,677	2688	2,544,261	516,481	903	11,729	178	159	7	1

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