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Table 1 Summary of the numbers of reads, identified genes, novel transcribed units, alternative splicing genes and extended genes

From: A global view of porcine transcriptome in three tissues from a full-sib pair with extreme phenotypes in growth and fat deposition by paired-end RNA sequencing

  2268 AF 2268 liver 2268 LD 2270 AF 2270 liver 2270 LD
total reads 40,000,000 38,808,956 39,020,950 40,000,000 40,133,362 39,164,798
total unmapped reads 14,293,709 13,771,813 14,076,474 15,445,291 14,285,367 13,457,962
reads perfectly matched to the reference genome 16,867,579 17,398,322 12,737,195 15,882,824 17,575,361 13,920,553
reads with < = 2 bp mismatch to the reference genome 8,838,712 7,638,821 12,207,281 8,671,885 8,272,634 11,786,283
reads uniquely matched to the reference genome 22,908,741 22,998,328 23,301,854 21,235,855 23,695,323 23,823,564
reads matched to the reference genome with multi-positions 2,797,550 2,038,815 1,642,622 3,318,854 2,152,672 1,883,272
annotated genes identified in this study 19,062 17,382 15,612 18,695 17,447 15,716
reads uniquely matched to annotated genes 8,508,418 9,465,873 8,615,406 9,075,466 10,219,332 9,530,691
reads matched to annotated genes with multi-positions 10,648,618 15,009,898 13,906,877 10,839,003 15,072,157 13,441,905
novel transcript units 122,931 71,394 48,045 112,052 72,401 69,677
clustered transcriptionally active regions 29,499 22,871 17,085 25,842 21,840 22,099
alternative splicing genes 2882 1,851 1,859 2,832 2,116 1,657
5' extended genes 815 610 587 793 697 593
3' extended genes 1,201 1,375 1,075 1,360 1,224 1,064
Genes extended both 5' and 3' ends 672 551 432 636 590 411