>>>> ConvertEnsembl <<<< Parameters: Project directory: convert/ensembl/rice Processing convert/ensembl/rice/Oryza_sativa.IRGSP-1.0.dna_sm.toplevel.fa.gz Chr01 1 43,270,923 Chr02 2 35,937,250 Chr03 3 36,413,819 Chr04 4 35,502,694 Chr05 5 29,958,434 Chr06 6 31,248,787 Chr07 7 29,697,621 Chr08 8 28,443,022 Chr09 9 23,012,720 Chr10 10 23,207,287 Chr11 11 29,021,106 Chr12 12 27,531,856 Finish writing /genomic.fa Finish writing /genomic.fa A 53,531,299 a 51,759,567 T 53,502,765 t 51,785,165 C 41,674,471 c 39,588,481 G 41,698,371 g 39,588,746 N 199 n 116,455 Gaps >= 30000: 0 (using N and n) Processing convert/ensembl/rice/Oryza_sativa.IRGSP-1.0.54.gff3.gz Use Genes 35,666 from 37,960 Use mRNAs 35,666 from 44,754 Use Exons 153,846 from 198,053 Finish writing /anno.gff >>Sequences 12 Chromosomes of 373,245,519 total length 2 Mt/Pt of 625,045 total length -- not written to file 49 Scaffolds of 1,178,721 total length (12<10,000bp) -- not written to file >>All Type (col 3) CDS 165,271 RNase_MRP_RNA 1 SRP_RNA 2 biological_region 546 chromosome 14 exon 198,053 * five_prime_UTR 45,615 gene 37,960 * lnc_RNA 95 mRNA 44,754 * ncRNA_gene 1,011 pre_miRNA 97 pseudogene 7 pseudogenic_transcript 7 rRNA 275 scaffold 49 snRNA 83 snoRNA 216 tRNA 242 three_prime_UTR 51,073 >>All Gene Source (col 2) DDBJ 53 * EMBL 58 * RAP2018-11-26 37,849 * >>All gene biotype= nontranslating_CDS 2,185 protein_coding 35,775 * >>Written to file Genes 35,666 mRNA 35,666 Exons 153,846 >>Chromosome gene count 35,666 Chr01 1 4,967 Chr02 2 3,981 Chr03 3 4,272 Chr04 4 3,157 Chr05 5 2,861 Chr06 6 2,971 Chr07 7 2,730 Chr08 8 2,439 Chr09 9 1,992 Chr10 10 1,980 Chr11 11 2,273 Chr12 12 2,043 Genes not on Chromosome 109 ConvertEnsembl completed