==> all_species_quality.txt <== ==> athaliana.txt <== # gffcompare v0.10.4 | Command line was: #/home/caitlin/software/gffcompare-0.10.4.Linux_x86_64/gffcompare -r ./genome/Araport11_GFF3_genes_transposons.201606.gff -o merged_cmp merged_transcripts.gtf # #= Summary for dataset: merged_transcripts.gtf # Query mRNAs : 61539 in 36907 loci (44265 multi-exon transcripts) # (11664 multi-transcript loci, ~1.7 transcripts per locus) # Reference mRNAs : 58980 in 36840 loci (43852 multi-exon) # Super-loci w/ reference transcripts: 36716 #-----------------| Sensitivity | Precision | Base level: 100.0 | 99.4 | Exon level: 100.0 | 98.8 | Intron level: 100.0 | 100.0 | Intron chain level: 100.0 | 99.1 | Transcript level: 100.0 | 95.8 | Locus level: 100.0 | 99.8 | Matching intron chains: 43852 Matching transcripts: 58980 Matching loci: 36840 Missed exons: 0/201142 ( 0.0%) Novel exons: 68/203941 ( 0.0%) Missed introns: 1/135763 ( 0.0%) Novel introns: 0/135763 ( 0.0%) Missed loci: 0/36840 ( 0.0%) Novel loci: 67/36907 ( 0.2%) Total union super-loci across all input datasets: 36907 61539 out of 61539 consensus transcripts written in merged_cmp.annotated.gtf (0 discarded as redundant) ==> atrichopoda.txt <== # gffcompare v0.10.4 | Command line was: #/home/caitlin/software/gffcompare-0.10.4.Linux_x86_64/gffcompare -r ./genome/Atrichopoda_291_v1.0.gene.gff3 -o merged_cmp merged_transcripts.gtf # #= Summary for dataset: merged_transcripts.gtf # Query mRNAs : 42209 in 37967 loci (17187 multi-exon transcripts) # (3550 multi-transcript loci, ~1.1 transcripts per locus) # Reference mRNAs : 26846 in 26845 loci (17187 multi-exon) # Super-loci w/ reference transcripts: 26262 #-----------------| Sensitivity | Precision | Base level: 100.0 | 53.4 | Exon level: 100.0 | 87.7 | Intron level: 99.5 | 99.5 | Intron chain level: 100.0 | 100.0 | Transcript level: 100.0 | 63.6 | Locus level: 100.0 | 70.6 | Matching intron chains: 17187 Matching transcripts: 26846 Matching loci: 26845 Missed exons: 0/109783 ( 0.0%) Novel exons: 11159/125146 ( 8.9%) Missed introns: 395/82937 ( 0.5%) Novel introns: 0/82937 ( 0.0%) Missed loci: 0/26845 ( 0.0%) Novel loci: 11000/37967 ( 29.0%) Total union super-loci across all input datasets: 37967 42209 out of 42209 consensus transcripts written in merged_cmp.annotated.gtf (0 discarded as redundant) ==> bhygrometrica.txt <== # gffcompare v0.10.4 | Command line was: #/home/caitlin/software/gffcompare-0.10.4.Linux_x86_64/gffcompare -r ./genome/GCA_001598015.1_Boea_hygrometrica.v1_genomic.gff -o merged_cmp merged_transcripts.gtf # #= Summary for dataset: merged_transcripts.gtf # Query mRNAs : 58547 in 56328 loci (32369 multi-exon transcripts) # (1989 multi-transcript loci, ~1.0 transcripts per locus) # Reference mRNAs : 47778 in 47778 loci (32369 multi-exon) # Super-loci w/ reference transcripts: 47777 #-----------------| Sensitivity | Precision | Base level: 100.0 | 92.3 | Exon level: 100.0 | 94.1 | Intron level: 100.0 | 100.0 | Intron chain level: 100.0 | 100.0 | Transcript level: 100.0 | 81.6 | Locus level: 100.0 | 84.8 | Matching intron chains: 32369 Matching transcripts: 47778 Matching loci: 47778 Missed exons: 0/173087 ( 0.0%) Novel exons: 8551/183856 ( 4.7%) Missed introns: 0/125309 ( 0.0%) Novel introns: 0/125309 ( 0.0%) Missed loci: 0/47778 ( 0.0%) Novel loci: 8524/56328 ( 15.1%) Total union super-loci across all input datasets: 56328 58547 out of 58547 consensus transcripts written in merged_cmp.annotated.gtf (0 discarded as redundant) ==> creinhardtii.txt <== # gffcompare v0.10.4 | Command line was: #/home/caitlin/software/gffcompare-0.10.4.Linux_x86_64/gffcompare -r ./genome/Creinhardtii_281_v5.5.gene.gff3 -o merged_cmp merged_transcripts.gtf # #= Summary for dataset: merged_transcripts.gtf # Query mRNAs : 21467 in 18128 loci (18434 multi-exon transcripts) # (2633 multi-transcript loci, ~1.2 transcripts per locus) # Reference mRNAs : 19198 in 17632 loci (18139 multi-exon) # Super-loci w/ reference transcripts: 17625 #-----------------| Sensitivity | Precision | Base level: 100.0 | 98.6 | Exon level: 100.0 | 98.6 | Intron level: 100.0 | 100.0 | Intron chain level: 100.0 | 98.4 | Transcript level: 100.0 | 89.4 | Locus level: 100.0 | 97.2 | Matching intron chains: 18139 Matching transcripts: 19198 Matching loci: 17632 Missed exons: 0/155267 ( 0.0%) Novel exons: 502/157529 ( 0.3%) Missed introns: 0/137240 ( 0.0%) Novel introns: 0/137240 ( 0.0%) Missed loci: 0/17632 ( 0.0%) Novel loci: 502/18128 ( 2.8%) Total union super-loci across all input datasets: 18128 21467 out of 21467 consensus transcripts written in merged_cmp.annotated.gtf (0 discarded as redundant) ==> esalsugineum.txt <== # gffcompare v0.10.4 | Command line was: #/home/caitlin/software/gffcompare-0.10.4.Linux_x86_64/gffcompare -r /1/scratch/caitlin/compPreds/esals/genome/Esalsugineum_173_v1.0.gene.gff3 -o merged_cmp merged_transcripts.gtf # #= Summary for dataset: merged_transcripts.gtf # Query mRNAs : 34863 in 27942 loci (24292 multi-exon transcripts) # (5325 multi-transcript loci, ~1.2 transcripts per locus) # Reference mRNAs : 29174 in 26347 loci (24183 multi-exon) # Super-loci w/ reference transcripts: 26299 #-----------------| Sensitivity | Precision | Base level: 100.0 | 92.7 | Exon level: 100.0 | 96.2 | Intron level: 100.0 | 100.0 | Intron chain level: 100.0 | 99.6 | Transcript level: 100.0 | 83.7 | Locus level: 100.0 | 94.2 | Matching intron chains: 24183 Matching transcripts: 29174 Matching loci: 26347 Missed exons: 0/144646 ( 0.0%) Novel exons: 1628/150324 ( 1.1%) Missed introns: 7/116988 ( 0.0%) Novel introns: 0/116988 ( 0.0%) Missed loci: 0/26347 ( 0.0%) Novel loci: 1607/27942 ( 5.8%) Total union super-loci across all input datasets: 27942 34863 out of 34863 consensus transcripts written in merged_cmp.annotated.gtf (0 discarded as redundant) ==> osativa.txt <== # gffcompare v0.10.4 | Command line was: #/home/caitlin/software/gffcompare-0.10.4.Linux_x86_64/gffcompare -r ./genome/Osativa_323_v7.0.gene.gff3 -o merged_cmp merged_transcripts.gtf # #= Summary for dataset: merged_transcripts.gtf # Query mRNAs : 66576 in 50281 loci (42077 multi-exon transcripts) # (9112 multi-transcript loci, ~1.3 transcripts per locus) # Reference mRNAs : 52352 in 42097 loci (42038 multi-exon) # Super-loci w/ reference transcripts: 42087 #-----------------| Sensitivity | Precision | Base level: 100.0 | 90.7 | Exon level: 100.0 | 93.4 | Intron level: 100.0 | 100.0 | Intron chain level: 100.0 | 99.9 | Transcript level: 100.0 | 78.6 | Locus level: 100.0 | 83.7 | Matching intron chains: 42038 Matching transcripts: 52352 Matching loci: 42097 Missed exons: 0/202019 ( 0.0%) Novel exons: 8187/216252 ( 3.8%) Missed introns: 4/151843 ( 0.0%) Novel introns: 0/151843 ( 0.0%) Missed loci: 0/42097 ( 0.0%) Novel loci: 7202/50281 ( 14.3%) Total union super-loci across all input datasets: 50281 66576 out of 66576 consensus transcripts written in merged_cmp.annotated.gtf (0 discarded as redundant) ==> ppatens.txt <== # gffcompare v0.10.4 | Command line was: #/home/caitlin/software/gffcompare-0.10.4.Linux_x86_64/gffcompare -r ./genome/Ppatens_318_v3.3.gene_X.gff3 -o merged_cmp merged_transcripts.gtf # #= Summary for dataset: merged_transcripts.gtf # Query mRNAs : 88657 in 31977 loci (76219 multi-exon transcripts) # (20429 multi-transcript loci, ~2.8 transcripts per locus) # Reference mRNAs : 78464 in 31468 loci (67906 multi-exon) # Super-loci w/ reference transcripts: 31402 #-----------------| Sensitivity | Precision | Base level: 100.0 | 99.5 | Exon level: 100.0 | 97.4 | Intron level: 100.0 | 100.0 | Intron chain level: 100.0 | 89.1 | Transcript level: 100.0 | 88.5 | Locus level: 100.0 | 98.4 | Matching intron chains: 67906 Matching transcripts: 78464 Matching loci: 31468 Missed exons: 0/237936 ( 0.0%) Novel exons: 509/252820 ( 0.2%) Missed introns: 10/160757 ( 0.0%) Novel introns: 0/160757 ( 0.0%) Missed loci: 0/31468 ( 0.0%) Novel loci: 502/31977 ( 1.6%) Total union super-loci across all input datasets: 31977 88657 out of 88657 consensus transcripts written in merged_cmp.annotated.gtf (0 discarded as redundant) ==> slycopersicum.txt <== # gffcompare v0.10.4 | Command line was: #/home/caitlin/software/gffcompare-0.10.4.Linux_x86_64/gffcompare -r ./genome/Slycopersicum_390_ITAG2.4.gene.gff3 -o merged_cmp merged_transcripts.gtf # #= Summary for dataset: merged_transcripts.gtf # Query mRNAs : 43966 in 39186 loci (26220 multi-exon transcripts) # (4189 multi-transcript loci, ~1.1 transcripts per locus) # Reference mRNAs : 34723 in 34373 loci (26218 multi-exon) # Super-loci w/ reference transcripts: 34321 #-----------------| Sensitivity | Precision | Base level: 100.0 | 88.0 | Exon level: 100.0 | 94.6 | Intron level: 99.9 | 99.9 | Intron chain level: 100.0 | 100.0 | Transcript level: 100.0 | 79.0 | Locus level: 100.0 | 87.7 | Matching intron chains: 26218 Matching transcripts: 34723 Matching loci: 34373 Missed exons: 0/160323 ( 0.0%) Novel exons: 4834/169564 ( 2.9%) Missed introns: 75/125542 ( 0.1%) Novel introns: 0/125542 ( 0.0%) Missed loci: 0/34373 ( 0.0%) Novel loci: 4828/39186 ( 12.3%) Total union super-loci across all input datasets: 39186 43966 out of 43966 consensus transcripts written in merged_cmp.annotated.gtf (0 discarded as redundant) ==> smoellendorffi.txt <== # gffcompare v0.10.4 | Command line was: #/home/caitlin/software/gffcompare-0.10.4.Linux_x86_64/gffcompare -r ./genome/Smoellendorffii_91_v1.0.gene.gff3 -o merged_cmp merged_transcripts.gtf # #= Summary for dataset: merged_transcripts.gtf # Query mRNAs : 33273 in 27354 loci (18800 multi-exon transcripts) # (5200 multi-transcript loci, ~1.2 transcripts per locus) # Reference mRNAs : 22284 in 22240 loci (18800 multi-exon) # Super-loci w/ reference transcripts: 21657 #-----------------| Sensitivity | Precision | Base level: 100.0 | 49.6 | Exon level: 100.0 | 91.9 | Intron level: 100.0 | 100.0 | Intron chain level: 100.0 | 100.0 | Transcript level: 100.0 | 67.0 | Locus level: 100.0 | 79.2 | Matching intron chains: 18800 Matching transcripts: 22284 Matching loci: 22240 Missed exons: 0/124630 ( 0.0%) Novel exons: 5697/135619 ( 4.2%) Missed introns: 0/102345 ( 0.0%) Novel introns: 0/102345 ( 0.0%) Missed loci: 0/22240 ( 0.0%) Novel loci: 5669/27354 ( 20.7%) Total union super-loci across all input datasets: 27354 33273 out of 33273 consensus transcripts written in merged_cmp.annotated.gtf (0 discarded as redundant) ==> stuberosum.txt <== # gffcompare v0.10.4 | Command line was: #/home/caitlin/software/gffcompare-0.10.4.Linux_x86_64/gffcompare -r ./genome/Stuberosum_448_v4.03.gene.gff3 -o merged_cmp merged_transcripts.gtf # #= Summary for dataset: merged_transcripts.gtf # Query mRNAs : 73675 in 58511 loci (36481 multi-exon transcripts) # (8704 multi-transcript loci, ~1.3 transcripts per locus) # Reference mRNAs : 52862 in 39301 loci (35981 multi-exon) # Super-loci w/ reference transcripts: 39112 #-----------------| Sensitivity | Precision | Base level: 100.0 | 83.3 | Exon level: 100.0 | 88.3 | Intron level: 100.0 | 100.0 | Intron chain level: 100.0 | 98.6 | Transcript level: 100.0 | 71.8 | Locus level: 100.0 | 67.2 | Matching intron chains: 35981 Matching transcripts: 52862 Matching loci: 39301 Missed exons: 0/151754 ( 0.0%) Novel exons: 19211/171906 ( 11.2%) Missed introns: 14/101589 ( 0.0%) Novel introns: 0/101589 ( 0.0%) Missed loci: 0/39301 ( 0.0%) Novel loci: 19185/58511 ( 32.8%) Total union super-loci across all input datasets: 58511 73675 out of 73675 consensus transcripts written in merged_cmp.annotated.gtf (0 discarded as redundant) ==> zmays.txt <== # gffcompare v0.10.4 | Command line was: #/home/caitlin/software/gffcompare-0.10.4.Linux_x86_64/gffcompare -r ./genome/Zmays_284_Ensembl-18_2010-01-MaizeSequence.gene.gff3 -o merged_cmp merged_transcripts.gtf # #= Summary for dataset: merged_transcripts.gtf # Query mRNAs : 95751 in 68568 loci (60101 multi-exon transcripts) # (14348 multi-transcript loci, ~1.4 transcripts per locus) # Reference mRNAs : 86192 in 63520 loci (58395 multi-exon) # Super-loci w/ reference transcripts: 63490 #-----------------| Sensitivity | Precision | Base level: 100.0 | 96.1 | Exon level: 100.0 | 96.8 | Intron level: 100.0 | 100.0 | Intron chain level: 100.0 | 97.2 | Transcript level: 100.0 | 90.0 | Locus level: 100.0 | 92.6 | Matching intron chains: 58395 Matching transcripts: 86192 Matching loci: 63520 Missed exons: 0/268218 ( 0.0%) Novel exons: 5053/277657 ( 1.8%) Missed introns: 11/183523 ( 0.0%) Novel introns: 0/183523 ( 0.0%) Missed loci: 0/63520 ( 0.0%) Novel loci: 5034/68568 ( 7.3%) Total union super-loci across all input datasets: 68568 95751 out of 95751 consensus transcripts written in merged_cmp.annotated.gtf (0 discarded as redundant)