gff3和gtf具体内容区别

gene的区别：39591+6812+27=46430
b73 gff3

awk '{print $3}' Zea_mays.B73_RefGen_v4.41.gff3 |sort |uniq -c
  46702 
    267 1
      1 B73
 924857 CDS
     12 chromosome
    255 contig
1211157 exon
 249764 five_prime_UTR
  39591 gene <-----------------------------------------------
   2591 lnc_RNA
    154 miRNA
 131585 mRNA
      1 ncRNA
   6812 ncRNA_gene <-----------------------------------------
    193 pre_miRNA
     27 pseudogene <-----------------------------------------
     27 pseudogenic_transcript
      1 RNase_MRP_RNA
    325 rRNA
    468 snoRNA
    179 snRNA
     66 SRP_RNA
 254056 three_prime_UTR
   2834 tRNA

b73 gtf

awk '{print $3}' Zea_mays.B73_RefGen_v4.41.gtf |sort |uniq -c 
      4 
 924111 CDS
1211157 exon
 249764 five_prime_utr
  46430 gene <-----------------------------------------------
      1 RefGen_v4
 131092 start_codon
 128946 stop_codon
 254056 three_prime_utr
 138424 transcript

w22 gff3

tail -946294 Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1.gff3 | awk '{print $3}'|sort |uniq -c
 277933 CDS
     10 chromosome
 313830 exon
  40691 gene <-----------------------------------------------
 262113 intron
  51717 mRNA

拟南芥 gtf

awk '{print $3}' Arabidopsis_thaliana.TAIR10.48.gtf |sort |uniq -c
      5 
 285977 CDS
 313952 exon
  56384 five_prime_utr
  32833 gene <-----------------------------------------------
  48315 start_codon
  48313 stop_codon
  48308 three_prime_utr
  54013 transcript

拟南芥 gff3

awk '{print $3}' Arabidopsis_thaliana.TAIR10.48.gff3 |sort |uniq -c
  32846 
      7 1
 286067 CDS
      7 chromosome
 313952 exon
  56384 five_prime_UTR
  27655 gene <-----------------------------------------------
   3879 lnc_RNA
    325 miRNA
  48359 mRNA
    377 ncRNA
   5178 ncRNA_gene <-----------------------------------------------
     15 rRNA
    287 snoRNA
     82 snRNA
  48308 three_prime_UTR
    689 tRNA

水稻 gtf

awk '{print $3}' Oryza_sativa.IRGSP-1.0.48.gtf |sort |uniq -c
      5 
 165166 CDS
 198053 exon
  45615 five_prime_utr
  38978 gene <-----------------------------------------------
  33170 start_codon
  40418 stop_codon
  51073 three_prime_utr
  45772 transcript

水稻 gff3

awk '{print $3}' Oryza_sativa.IRGSP-1.0.48.gff3 |sort |uniq -c
  39047 
     63 1
    546 biological_region
 165271 CDS
     14 chromosome
 198053 exon
  45615 five_prime_UTR
  37960 gene <-----------------------------------------------
     95 lnc_RNA
  44754 mRNA
   1011 ncRNA_gene <-----------------------------------------------
     97 pre_miRNA
      7 pseudogene <-----------------------------------------------
      7 pseudogenic_transcript
      1 RNase_MRP_RNA
    275 rRNA
     49 scaffold
    216 snoRNA
     83 snRNA
      2 SRP_RNA
  51073 three_prime_UTR
    242 tRNA