Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes

BMC Genomics

Table 2 Summary of annotation of consensus filtered InDels based on Ensembl gene annotations (release 71)

	Count	Percent (%)
Total number of InDels	883,570
Annotation possible	886,116	100
Alternate annotation	2,546	0.29
Annotation result
Intergenic	438,714	49.51
Intronic	409,956	46.26
Exonic	1,088	0.12
frameshift deletion	270	0.03
frameshift insertion	333	0.04
frameshift substitution	10	>0.01
non-frameshift deletion	301	0.03
non-frameshift insertion	162	0.02
non-frameshift substitution	2	>0.01
stop-gain/stop-loss	10	>0.01
1 kb downstream	13,854	1.56
1 kb upstream	9,959	1.12
UTR3	11,488	1.30
UTR5	819	0.09
Splicing	162	0.02
Non-coding RNA (ncRNA)	85^a	0.01

^aIncludes 9 ncRNA variants that were detected by annotation against novel ncRNA transcripts [71]

ISSN: 1471-2164