Oryza_sativa

Clones by site

site htg_phase count(*)
0 11
3 15
AGI(USA) 0 1
AGI(USA) 3 44
ASPGC(Taiwan) 0 30
ASPGC(Taiwan) 3 290
BIOTEC(Thailand) 0 6
BIOTEC(Thailand) 3 2
CSHL(USA) 0 4
CSHL(USA) 3 114
CUGI(USA) 0 3
CUGI(USA) 3 92
GCW(USA) 3 3
Genoscope(France) 0 21
Genoscope(France) 3 281
IIRGS(India) 0 16
IIRGS(India) 3 117
KRGRP(Korea) 0 22
KRGRP(Korea) 3 10
LGBUGA(USA) 3 3
NCGR(China) 0 71
NCGR(China) 3 299
PGIR(USA) 0 1
PGIR(USA) 3 47
RGP(Japan) 0 288
RGP(Japan) 3 1843
TIGR(USA) 0 39
TIGR(USA) 3 457

site	htg_phase	count(*)
	0	11
	3	15
AGI(USA)	0	1
AGI(USA)	3	44
ASPGC(Taiwan)	0	30
ASPGC(Taiwan)	3	290
BIOTEC(Thailand)	0	6
BIOTEC(Thailand)	3	2
CSHL(USA)	0	4
CSHL(USA)	3	114
CUGI(USA)	0	3
CUGI(USA)	3	92
GCW(USA)	3	3
Genoscope(France)	0	21
Genoscope(France)	3	281
IIRGS(India)	0	16
IIRGS(India)	3	117
KRGRP(Korea)	0	22
KRGRP(Korea)	3	10
LGBUGA(USA)	3	3
NCGR(China)	0	71
NCGR(China)	3	299
PGIR(USA)	0	1
PGIR(USA)	3	47
RGP(Japan)	0	288
RGP(Japan)	3	1843
TIGR(USA)	0	39
TIGR(USA)	3	457

Clones by phase

htg_phase count(*)
0 513
3 3617

htg_phase	count(*)
0	513
3	3617

Sequence size

min(name) sum(asm_end-asm_start)
1 43243189
2 35871011
3 36342477
4 35018456
5 29688576
6 31196344
7 29686314
8 28307908
9 22672472
10 22691174
11 28363142
12 27491282
R4_AL606632 163731
R4_AL606458 144802
R4_AL606594 173163
R4_AL606604 150180
R5_AC136222 153367
R5_AC108501 156162
R11_AC135957 131578
R11_AC137923 134721
R12_BX255875 151202
R12_AL713950 103306
1 372034557

min(name)	sum(asm_end-asm_start)
1	43243189
2	35871011
3	36342477
4	35018456
5	29688576
6	31196344
7	29686314
8	28307908
9	22672472
10	22691174
11	28363142
12	27491282
R4_AL606632	163731
R4_AL606458	144802
R4_AL606594	173163
R4_AL606604	150180
R5_AC136222	153367
R5_AC108501	156162
R11_AC135957	131578
R11_AC137923	134721
R12_BX255875	151202
R12_AL713950	103306
1	372034557

Contig totals

name count(*) sum(length) min(length) max(length)
chromosome 22 372093005 103307 43249587
clone 4130 576159227 713 354587

name	count(*)	sum(length)	min(length)	max(length)
chromosome	22	372093005	103307	43249587
clone	4130	576159227	713	354587

Contigs by Chromosome

chrnum count(*) sum(length)
0 10 1146791
1 442 63976768
2 439 59569338
3 352 48614722
4 363 49501890
5 325 44099447
6 336 44691077
7 365 48966432
8 345 48604168
9 270 37652003
10 297 52948295
11 289 39463406
12 297 36924890

chrnum	count(*)	sum(length)
0	10	1146791
1	442	63976768
2	439	59569338
3	352	48614722
4	363	49501890
5	325	44099447
6	336	44691077
7	365	48966432
8	345	48604168
9	270	37652003
10	297	52948295
11	289	39463406
12	297	36924890

Total Genes

count(*)
121153

count(*)
121153

Genes by Analysis

program ngene
Submitter_tRNA_Annotation 171
SubmitterGeneAnnotation 62230
tigr 58752

program	ngene
Submitter_tRNA_Annotation	171
SubmitterGeneAnnotation	62230
tigr	58752

Genes by type

type count(*)
known 62401
TE-like 14196
tigr 44556

type	count(*)
known	62401
TE-like	14196
tigr	44556

Number of Transcripts, Number of Translations

count()
124493
count()
124322

count(*)
124493

count(*)
124322

Number of Exons

count()
494876
name min(seq_region_end-seq_region_start+1) avg(seq_region_end-seq_region_start+1) max(seq_region_end-seq_region_start+1) count()
chromosome 1 349.3509 15363 261415
clone 4 282.9544 17928 233461

count(*)
494876

name	min(seq_region_end-seq_region_start+1)	avg(seq_region_end-seq_region_start+1)	max(seq_region_end-seq_region_start+1)	count(*)
chromosome	1	349.3509	15363	261415
clone	4	282.9544	17928	233461

Exon Sizes

name min(seq_region_end-seq_region_start+1) avg(seq_region_end-seq_region_start+1) max(seq_region_end-seq_region_start+1) count(*)
chromosome 1 349.3509 15363 261415
clone 4 282.9544 17928 233461

name	min(seq_region_end-seq_region_start+1)	avg(seq_region_end-seq_region_start+1)	max(seq_region_end-seq_region_start+1)	count(*)
chromosome	1	349.3509	15363	261415
clone	4	282.9544	17928	233461

Count of transcripts by number of exons

exons count(*)
1 29303
2 30283
3 17300
4 10837
5 7982
6 6060
7 4988
8 3736
9 2875
10 2311
11 1805
12 1494
13 1134
14 872
15 677
16 539
17 393
18 375
19 288
20 236
21 184
22 165
23 123
24 94
25 68
26 42
27 45
28 28
29 33
30 26
31 28
32 15
33 15
34 30
35 8
36 6
37 16
38 23
39 3
40 5
41 4
42 6
43 2
44 2
45 1
46 2
47 2
48 3
49 4
50 5
51 2
52 3
56 2
57 1
59 3
63 1
64 2
69 1
73 1
76 1

exons	count(*)
1	29303
2	30283
3	17300
4	10837
5	7982
6	6060
7	4988
8	3736
9	2875
10	2311
11	1805
12	1494
13	1134
14	872
15	677
16	539
17	393
18	375
19	288
20	236
21	184
22	165
23	123
24	94
25	68
26	42
27	45
28	28
29	33
30	26
31	28
32	15
33	15
34	30
35	8
36	6
37	16
38	23
39	3
40	5
41	4
42	6
43	2
44	2
45	1
46	2
47	2
48	3
49	4
50	5
51	2
52	3
56	2
57	1
59	3
63	1
64	2
69	1
73	1
76	1

Number of external cross references for each type of object

ensembl_object_type count(*)
Transcript 212978
Gene 228049
Translation 74376

ensembl_object_type	count(*)
Transcript	212978
Gene	228049
Translation	74376

Number of external cross references by destination

db_name xcount
SWISSPROT 664
GO 1210
EGAD 10
GP 4710
PF 1525
PIR 1209
TIGR_FN 120844
TIGR_TU 58752
TIGR_MODEL 62149
TIGR 446
TIGR_LOCUS 126310
GRAMENE_OLD 52139
Interpro 3537

db_name	xcount
SWISSPROT	664
GO	1210
EGAD	10
GP	4710
PF	1525
PIR	1209
TIGR_FN	120844
TIGR_TU	58752
TIGR_MODEL	62149
TIGR	446
TIGR_LOCUS	126310
GRAMENE_OLD	52139
Interpro	3537

Prediction Transcripts

logic_name gff_feature gff_source program npt
fgenesh prediction FgenesH:Monocot fgenesh 56170

logic_name	gff_feature	gff_source	program	npt
fgenesh	prediction	FgenesH:Monocot	fgenesh	56170

Feature hits by type

fcount is number of features, hcount is number of hits

logic_name fcount hcount
Barley_ArrayTarget_Affy22K 11085 46964
Barley_GI 23289 81013
Barley_est 226813 621408
Barley_tug 13415 32187
Hvulgare_TUG_PlantGDB 25898 80667
Maize_ArrayConsensus_Affy18K 8874 43591
Maize_ArrayTarget_Affy18K 10132 46057
Maize_ArrayTarget_NSF58K 29015 105162
Maize_BACend 69556 140373
Maize_CDs 2125 9111
Maize_GI 23805 83519
Maize_MAGI_ISU 45146 127661
Maize_Mu_Insert 29693 49581
Maize_Unigene_Panzea 2125 9111
Maize_cornsensus 6789 28495
Maize_est 176974 472957
Maize_hi_cot_Bennetzen 74001 146247
Maize_hi_cot_TIGR 34722 83705
Maize_markers 2740 11353
Maize_meth_filt_CSHL_Mccombie 12539 22554
Maize_meth_filt_TIGR 127951 258223
Maize_meth_filt_hi_cot_cluster 52746 144282
Maize_tug 8307 19967
Millet_est 694 1828
Osativa_TUG_PlantGDB 41424 107263
Rice_Alta_BACend 13901 24247
Rice_ArrayConsensus_Affy57K 42616 172384
Rice_ArrayOligo_NSF20K 18884 23949
Rice_ArrayTarget_Affy57K 47729 173350
Rice_Australiensis_BACend 79873 141410
Rice_BAC 596 670
Rice_Brachyantha_BACend 36419 62597
Rice_CDS 1932 7836
Rice_Ds_Insert 1809 1834
Rice_FstTransposon 2486 2515
Rice_GI 52587 184825
Rice_Glaberrima_BACend 49302 53727
Rice_Japonica_BACend 51194 54348
Rice_MpssTag 92735 92735
Rice_Nivara_BACend 77230 85822
Rice_Punctata_BACend 50402 85121
Rice_Rufipogon_BACend 53412 58645
Rice_T_DNA_Insert 5847 5924
Rice_est 203849 477103
Rice_ind_cluster 20041 53041
Rice_ind_est 68779 153602
Rice_jap_cDNA_KOME 26832 118514
Rice_rflp_marker_non_rice 528 1403
Rice_rflp_marker_rice 2576 5218
Rice_tos17_insert 16478 16856
Rice_transposon_insert_site 1012 1024
Rice_tug 26150 52666
Rice_unmapped_BAC_back 673 909
Rice_unmapped_BAC_front 676 978
Ryegrass_Assembly 24342 53388
Ryegrass_Sequence 43906 79755
Sbicolor_TUG_PlantGDB 12633 36764
Sorghum_CDNA 1867 5120
Sorghum_GI 20025 65391
Sorghum_Markers 731 1815
Sorghum_cluster_Pratt 11712 30157
Sorghum_est 134242 350987
Sorghum_gss-read_Klein 117 234
Sorghum_orion 35693 84159
Sorghum_tug 4967 11540
Sugarcane_est 151942 436430
Taestivum_TUG_PlantGDB 33437 95302
Wheat_ArrayConsensus_Affy61K 19013 73700
Wheat_ArrayTarget_Affy61K 21616 77470
Wheat_GI 47343 147034
Wheat_est 312523 868944
Wheat_markers 3458 9268
Wheat_tug 33437 95302
Zmays_TUG_PlantGDB 24207 74485
riceAlta_bacends_omap 13901 24407
riceAustraliensis_bacends_omap 79873 142458
riceBrachyantha_bacends_omap 36419 63082
riceGlaberrima_bacends_omap 49302 53727
riceNivara_bacends_omap 77230 85822
ricePunctata_bacends_omap 50402 85543
riceRufipogon_bacends_omap 53412 58645
riceSativa_bacends_omap 51194 54348

logic_name	fcount	hcount
Barley_ArrayTarget_Affy22K	11085	46964
Barley_GI	23289	81013
Barley_est	226813	621408
Barley_tug	13415	32187
Hvulgare_TUG_PlantGDB	25898	80667
Maize_ArrayConsensus_Affy18K	8874	43591
Maize_ArrayTarget_Affy18K	10132	46057
Maize_ArrayTarget_NSF58K	29015	105162
Maize_BACend	69556	140373
Maize_CDs	2125	9111
Maize_GI	23805	83519
Maize_MAGI_ISU	45146	127661
Maize_Mu_Insert	29693	49581
Maize_Unigene_Panzea	2125	9111
Maize_cornsensus	6789	28495
Maize_est	176974	472957
Maize_hi_cot_Bennetzen	74001	146247
Maize_hi_cot_TIGR	34722	83705
Maize_markers	2740	11353
Maize_meth_filt_CSHL_Mccombie	12539	22554
Maize_meth_filt_TIGR	127951	258223
Maize_meth_filt_hi_cot_cluster	52746	144282
Maize_tug	8307	19967
Millet_est	694	1828
Osativa_TUG_PlantGDB	41424	107263
Rice_Alta_BACend	13901	24247
Rice_ArrayConsensus_Affy57K	42616	172384
Rice_ArrayOligo_NSF20K	18884	23949
Rice_ArrayTarget_Affy57K	47729	173350
Rice_Australiensis_BACend	79873	141410
Rice_BAC	596	670
Rice_Brachyantha_BACend	36419	62597
Rice_CDS	1932	7836
Rice_Ds_Insert	1809	1834
Rice_FstTransposon	2486	2515
Rice_GI	52587	184825
Rice_Glaberrima_BACend	49302	53727
Rice_Japonica_BACend	51194	54348
Rice_MpssTag	92735	92735
Rice_Nivara_BACend	77230	85822
Rice_Punctata_BACend	50402	85121
Rice_Rufipogon_BACend	53412	58645
Rice_T_DNA_Insert	5847	5924
Rice_est	203849	477103
Rice_ind_cluster	20041	53041
Rice_ind_est	68779	153602
Rice_jap_cDNA_KOME	26832	118514
Rice_rflp_marker_non_rice	528	1403
Rice_rflp_marker_rice	2576	5218
Rice_tos17_insert	16478	16856
Rice_transposon_insert_site	1012	1024
Rice_tug	26150	52666
Rice_unmapped_BAC_back	673	909
Rice_unmapped_BAC_front	676	978
Ryegrass_Assembly	24342	53388
Ryegrass_Sequence	43906	79755
Sbicolor_TUG_PlantGDB	12633	36764
Sorghum_CDNA	1867	5120
Sorghum_GI	20025	65391
Sorghum_Markers	731	1815
Sorghum_cluster_Pratt	11712	30157
Sorghum_est	134242	350987
Sorghum_gss-read_Klein	117	234
Sorghum_orion	35693	84159
Sorghum_tug	4967	11540
Sugarcane_est	151942	436430
Taestivum_TUG_PlantGDB	33437	95302
Wheat_ArrayConsensus_Affy61K	19013	73700
Wheat_ArrayTarget_Affy61K	21616	77470
Wheat_GI	47343	147034
Wheat_est	312523	868944
Wheat_markers	3458	9268
Wheat_tug	33437	95302
Zmays_TUG_PlantGDB	24207	74485
riceAlta_bacends_omap	13901	24407
riceAustraliensis_bacends_omap	79873	142458
riceBrachyantha_bacends_omap	36419	63082
riceGlaberrima_bacends_omap	49302	53727
riceNivara_bacends_omap	77230	85822
ricePunctata_bacends_omap	50402	85543
riceRufipogon_bacends_omap	53412	58645
riceSativa_bacends_omap	51194	54348

Marker hits by type

mcount=markers, hcount=hits

mtype logic_name program mcount hcount
est Rice_rflp_marker NULL 6612 6614
tos17 Rice_tos17_insert NULL 16478 16856
microsatellite Rice_SSR NULL 2660 3126

mtype	logic_name	program	mcount	hcount
est	Rice_rflp_marker	NULL	6612	6614
tos17	Rice_tos17_insert	NULL	16478	16856
microsatellite	Rice_SSR	NULL	2660	3126

Repeat Feature hits by type

ccount=consensuses, hcount=hits

logic_name program ccount hcount
Rice_TE NULL 57 11619

logic_name	program	ccount	hcount
Rice_TE	NULL	57	11619

Zea_mays

Clones by site

Clones by phase

Sequence size

min(name) sum(asm_end-asm_start)
1 214765510
10 114503652
2 187580374
3 183721938
4 199417804
5 171048909
6 116031455
7 121458656
8 127352791
9 100151268
? 17760245
UNKNOWN 242192040
1 1795984642

min(name)	sum(asm_end-asm_start)
1	214765510
10	114503652
2	187580374
3	183721938
4	199417804
5	171048909
6	116031455
7	121458656
8	127352791
9	100151268
?	17760245
UNKNOWN	242192040
1	1795984642

Contig totals

name count(*) sum(length) min(length) max(length)
chromosome 12 1795985408 17760256 242192384
fpc 766 1795985408 36864 19161088

name	count(*)	sum(length)	min(length)	max(length)
chromosome	12	1795985408	17760256	242192384
fpc	766	1795985408	36864	19161088

Contigs by Chromosome

Total Genes

count(*)
0

count(*)
0

Genes by Analysis

Genes by type

Number of Transcripts, Number of Translations

count()
0
count()
0

count(*)
0

count(*)
0

Number of Exons

count(*)
0

count(*)
0

Exon Sizes

Count of transcripts by number of exons

Number of external cross references for each type of object

Number of external cross references by destination

Prediction Transcripts

Feature hits by type

fcount is number of features, hcount is number of hits

Marker hits by type

mcount=markers, hcount=hits

mtype logic_name program mcount hcount
microsatellite Maize_marker NULL 19232 67243

mtype	logic_name	program	mcount	hcount
microsatellite	Maize_marker	NULL	19232	67243

Repeat Feature hits by type

ccount=consensuses, hcount=hits

Zea_mays2

Clones by site

Clones by phase

Sequence size

Contig totals

name count(*) sum(length) min(length) max(length)
clone 486 80220546 690 478466

name	count(*)	sum(length)	min(length)	max(length)
clone	486	80220546	690	478466

Contigs by Chromosome

Total Genes

count(*)
12632

count(*)
12632

Genes by Analysis

program ngene
fgenesh 12632

program	ngene
fgenesh	12632

Genes by type

type count(*)
12632

type	count(*)
	12632

Number of Transcripts, Number of Translations

count()
12632
count()
12632

count(*)
12632

count(*)
12632

Number of Exons

count()
50699
name min(seq_region_end-seq_region_start+1) avg(seq_region_end-seq_region_start+1) max(seq_region_end-seq_region_start+1) count()
clone 1 484.5918 5670 50699

count(*)
50699

name	min(seq_region_end-seq_region_start+1)	avg(seq_region_end-seq_region_start+1)	max(seq_region_end-seq_region_start+1)	count(*)
clone	1	484.5918	5670	50699

Exon Sizes

name min(seq_region_end-seq_region_start+1) avg(seq_region_end-seq_region_start+1) max(seq_region_end-seq_region_start+1) count(*)
clone 1 484.5918 5670 50699

name	min(seq_region_end-seq_region_start+1)	avg(seq_region_end-seq_region_start+1)	max(seq_region_end-seq_region_start+1)	count(*)
clone	1	484.5918	5670	50699

Count of transcripts by number of exons

exons count(*)
1 9171
2 11440
3 8566
4 6452
5 4811
6 3578
7 2349
8 1751
9 1157
10 729
11 592
12 468
13 354
14 239
15 166
16 107
17 117
18 68
19 67
20 44
21 12
22 36
23 8
24 4
25 16
28 4
30 4
31 12
32 8
38 4
41 4
50 4

exons	count(*)
1	9171
2	11440
3	8566
4	6452
5	4811
6	3578
7	2349
8	1751
9	1157
10	729
11	592
12	468
13	354
14	239
15	166
16	107
17	117
18	68
19	67
20	44
21	12
22	36
23	8
24	4
25	16
28	4
30	4
31	12
32	8
38	4
41	4
50	4

Number of external cross references for each type of object

ensembl_object_type count(*)
Translation 15351

ensembl_object_type	count(*)
Translation	15351

Number of external cross references by destination

db_name xcount
GO 450
Interpro 957

db_name	xcount
GO	450
Interpro	957

Prediction Transcripts

Feature hits by type

fcount is number of features, hcount is number of hits

logic_name fcount hcount
Barley1_GeneChip_exemplars 1306 4526
Barley_GI 2505 7689
Barley_est 28794 67244
Barley_tug 1865 3668
Maize_CDs_panzea 124 453
Maize_GI 2501 7522
Maize_ISU_MAGIs_3_1_w_singleton 7470 9283
Maize_Mu_Insert 10787 14903
Maize_consensus_Aff 424 1520
Maize_cornsensus 224 1091
Maize_est 27131 63595
Maize_hi_cot_Bennetzen 27771 34246
Maize_hi_cot_TIGR 11793 15278
Maize_markers 406 1355
Maize_meth_filt_CSHL_Mccombie 12158 17314
Maize_meth_filt_TIGR 59204 86313
Maize_meth_filt_hi_cot_cluster 36274 54507
Maize_tug 1524 3229
Millet_est 172 341
Rice_Alta_BACend 1135 2303
Rice_Australiensis_BACend 12689 26778
Rice_Brachyantha_BACend 3449 5989
Rice_CDS 455 2057
Rice_Ds_Insert 38 56
Rice_GI 5126 19718
Rice_Glaberrima_BACend 3604 5848
Rice_Japonica_BACend 5116 8420
Rice_Nivara_BACend 8061 14017
Rice_Punctata_BACend 4206 8456
Rice_Rufipogon_BACend 5039 9056
Rice_T_DNA_Insert 51 82
Rice_consensus_Aff 173 321
Rice_est 15057 38765
Rice_ind_cluster 1189 3822
Rice_ind_est 4185 10069
Rice_jap_cDNA_KOME 3450 14025
Rice_rflp_marker_non_rice 140 296
Rice_rflp_marker_rice 144 327
Rice_tos17_insert 352 610
Rice_transposon_insert_site 17 24
Rice_tug 1922 4294
Ryegrass_Assembly 4466 9395
Ryegrass_Sequence 6856 12782
Sorghum_CDNA 374 981
Sorghum_GI 3522 10806
Sorghum_Markers 164 382
Sorghum_cluster_Pratt 2098 5466
Sorghum_est 23270 59786
Sorghum_gss-read_Klein 21 30
Sorghum_orion 13358 29356
Sorghum_tug 944 2343
Sugarcane_est 25721 75783
Wheat_GI 5517 14828
Wheat_consensus_Aff 511 1238
Wheat_est 40605 97988
Wheat_markers 300 743
Wheat_tug 3762 9819

logic_name	fcount	hcount
Barley1_GeneChip_exemplars	1306	4526
Barley_GI	2505	7689
Barley_est	28794	67244
Barley_tug	1865	3668
Maize_CDs_panzea	124	453
Maize_GI	2501	7522
Maize_ISU_MAGIs_3_1_w_singleton	7470	9283
Maize_Mu_Insert	10787	14903
Maize_consensus_Aff	424	1520
Maize_cornsensus	224	1091
Maize_est	27131	63595
Maize_hi_cot_Bennetzen	27771	34246
Maize_hi_cot_TIGR	11793	15278
Maize_markers	406	1355
Maize_meth_filt_CSHL_Mccombie	12158	17314
Maize_meth_filt_TIGR	59204	86313
Maize_meth_filt_hi_cot_cluster	36274	54507
Maize_tug	1524	3229
Millet_est	172	341
Rice_Alta_BACend	1135	2303
Rice_Australiensis_BACend	12689	26778
Rice_Brachyantha_BACend	3449	5989
Rice_CDS	455	2057
Rice_Ds_Insert	38	56
Rice_GI	5126	19718
Rice_Glaberrima_BACend	3604	5848
Rice_Japonica_BACend	5116	8420
Rice_Nivara_BACend	8061	14017
Rice_Punctata_BACend	4206	8456
Rice_Rufipogon_BACend	5039	9056
Rice_T_DNA_Insert	51	82
Rice_consensus_Aff	173	321
Rice_est	15057	38765
Rice_ind_cluster	1189	3822
Rice_ind_est	4185	10069
Rice_jap_cDNA_KOME	3450	14025
Rice_rflp_marker_non_rice	140	296
Rice_rflp_marker_rice	144	327
Rice_tos17_insert	352	610
Rice_transposon_insert_site	17	24
Rice_tug	1922	4294
Ryegrass_Assembly	4466	9395
Ryegrass_Sequence	6856	12782
Sorghum_CDNA	374	981
Sorghum_GI	3522	10806
Sorghum_Markers	164	382
Sorghum_cluster_Pratt	2098	5466
Sorghum_est	23270	59786
Sorghum_gss-read_Klein	21	30
Sorghum_orion	13358	29356
Sorghum_tug	944	2343
Sugarcane_est	25721	75783
Wheat_GI	5517	14828
Wheat_consensus_Aff	511	1238
Wheat_est	40605	97988
Wheat_markers	300	743
Wheat_tug	3762	9819

Marker hits by type

mcount=markers, hcount=hits

Repeat Feature hits by type

ccount=consensuses, hcount=hits

Arabidopsis_thaliana

Clones by site

Clones by phase

Sequence size

min(name) sum(asm_end-asm_start)
1 30431172
2 19703100
3 23467471
4 18581833
5 26989310
1 119172886

min(name)	sum(asm_end-asm_start)
1	30431172
2	19703100
3	23467471
4	18581833
5	26989310
1	119172886

Contig totals

name count(*) sum(length) min(length) max(length)
chromosome 5 119186497 18585042 30432563
contig 1611 135187985 444 1874423

name	count(*)	sum(length)	min(length)	max(length)
chromosome	5	119186497	18585042	30432563
contig	1611	135187985	444	1874423

Contigs by Chromosome

Total Genes

count(*)
29993

count(*)
29993

Genes by Analysis

program ngene
NULL 29993

program	ngene
NULL	29993

Genes by type

type count(*)
Gene 26207
Pseudogene 3786

type	count(*)
Gene	26207
Pseudogene	3786

Number of Transcripts, Number of Translations

count()
32739
count()
32739

count(*)
32739

count(*)
32739

Number of Exons

count()
156461
name min(seq_region_end-seq_region_start+1) avg(seq_region_end-seq_region_start+1) max(seq_region_end-seq_region_start+1) count()
chromosome 1 327.9428 15195 156461

count(*)
156461

name	min(seq_region_end-seq_region_start+1)	avg(seq_region_end-seq_region_start+1)	max(seq_region_end-seq_region_start+1)	count(*)
chromosome	1	327.9428	15195	156461

Exon Sizes

name min(seq_region_end-seq_region_start+1) avg(seq_region_end-seq_region_start+1) max(seq_region_end-seq_region_start+1) count(*)
chromosome 1 327.9428 15195 156461

name	min(seq_region_end-seq_region_start+1)	avg(seq_region_end-seq_region_start+1)	max(seq_region_end-seq_region_start+1)	count(*)
chromosome	1	327.9428	15195	156461

Count of transcripts by number of exons

exons count(*)
1 9009
2 4243
3 3393
4 2787
5 2397
6 1865
7 1652
8 1257
9 1169
10 951
11 710
12 664
13 569
14 449
15 295
16 207
17 185
18 171
19 145
20 110
21 82
22 67
23 83
24 50
25 26
26 34
27 26
28 20
29 9
30 11
31 14
32 15
33 9
34 9
35 7
36 4
37 2
38 5
39 7
40 2
41 4
42 8
44 2
45 1
46 1
48 1
49 4
50 1
53 1
54 1
56 1
58 1
64 1
73 1
79 1

Number of external cross references for each type of object

ensembl_object_type count(*)
Transcript 286999
Gene 29993

Number of external cross references by destination

db_name xcount
GO 2175
Interpro 5843
TIGR 62732
SEEDS 123529
AFFY_ATH1 21625
AFFY_AG 7966
CATMA_TIGR5 21889

Prediction Transcripts

Feature hits by type

fcount is number of features, hcount is number of hits

logic_name fcount hcount
Affy_AG 8044 8044
Affy_ATH1 21764 21764
Brassica_EST 39253 39253
CATMA_TIGR5 21891 21893

Marker hits by type

mcount=markers, hcount=hits

Repeat Feature hits by type

ccount=consensuses, hcount=hits

exons	count(*)
1	9009
2	4243
3	3393
4	2787
5	2397
6	1865
7	1652
8	1257
9	1169
10	951
11	710
12	664
13	569
14	449
15	295
16	207
17	185
18	171
19	145
20	110
21	82
22	67
23	83
24	50
25	26
26	34
27	26
28	20
29	9
30	11
31	14
32	15
33	9
34	9
35	7
36	4
37	2
38	5
39	7
40	2
41	4
42	8
44	2
45	1
46	1
48	1
49	4
50	1
53	1
54	1
56	1
58	1
64	1
73	1
79	1

db_name	xcount
GO	2175
Interpro	5843
TIGR	62732
SEEDS	123529
AFFY_ATH1	21625
AFFY_AG	7966
CATMA_TIGR5	21889

logic_name	fcount	hcount
Affy_AG	8044	8044
Affy_ATH1	21764	21764
Brassica_EST	39253	39253
CATMA_TIGR5	21891	21893

Oryza_sativa

Clones by site

Clones by phase

htg_phasecount(*)051333617

Sequence size

Contig totals

namecount(*)sum(length)min(length)max(length)chromosome2237209300510330743249587clone4130576159227713354587

Contigs by Chromosome

chrnumcount(*)sum(length)0101146791144263976768243959569338335248614722436349501890532544099447633644691077736548966432834548604168927037652003102975294829511289394634061229736924890

Total Genes

count(*)121153

Genes by Analysis

programngeneSubmitter_tRNA_Annotation171SubmitterGeneAnnotation62230tigr58752

Genes by type

typecount(*)known62401TE-like14196tigr44556

Number of Transcripts, Number of Translations

count(*)124493count(*)124322

Number of Exons

count(*)494876namemin(seq_region_end-seq_region_start+1)avg(seq_region_end-seq_region_start+1)max(seq_region_end-seq_region_start+1)count(*)chromosome1349.350915363261415clone4282.954417928233461

Exon Sizes

namemin(seq_region_end-seq_region_start+1)avg(seq_region_end-seq_region_start+1)max(seq_region_end-seq_region_start+1)count(*)chromosome1349.350915363261415clone4282.954417928233461

Count of transcripts by number of exons

exonscount(*)1293032302833173004108375798266060749888373692875102311111805121494131134148721567716539173931837519288202362118422165231232494256826422745282829333026312832153315343035836637163823393405414426432442451462472483494505512523562571593631642691731761

Number of external cross references for each type of object

ensembl_object_typecount(*)Transcript212978Gene228049Translation74376

Number of external cross references by destination

db_namexcountSWISSPROT664GO1210EGAD10GP4710PF1525PIR1209TIGR_FN120844TIGR_TU58752TIGR_MODEL62149TIGR446TIGR_LOCUS126310GRAMENE_OLD52139Interpro3537

Prediction Transcripts

logic_namegff_featuregff_sourceprogramnptfgeneshpredictionFgenesH:Monocotfgenesh56170

Feature hits by type

fcount is number of features, hcount is number of hits

Marker hits by type

mcount=markers, hcount=hits

mtypelogic_nameprogrammcounthcountestRice_rflp_markerNULL66126614tos17Rice_tos17_insertNULL1647816856microsatelliteRice_SSRNULL26603126

Repeat Feature hits by type

ccount=consensuses, hcount=hits

logic_nameprogramccounthcountRice_TENULL5711619

Zea_mays

Clones by site

Clones by phase

Sequence size

min(name)sum(asm_end-asm_start)12147655101011450365221875803743183721938419941780451710489096116031455712145865681273527919100151268?17760245UNKNOWN24219204011795984642

Contig totals

namecount(*)sum(length)min(length)max(length)chromosome12179598540817760256242192384fpc76617959854083686419161088

Contigs by Chromosome

Total Genes

count(*)0

Genes by Analysis

Genes by type

Number of Transcripts, Number of Translations

count(*)0count(*)0

Number of Exons

count(*)0

Exon Sizes

Count of transcripts by number of exons

Number of external cross references for each type of object

Number of external cross references by destination

Prediction Transcripts

Feature hits by type

fcount is number of features, hcount is number of hits

Marker hits by type

mcount=markers, hcount=hits

mtypelogic_nameprogrammcounthcountmicrosatelliteMaize_markerNULL1923267243

Repeat Feature hits by type

ccount=consensuses, hcount=hits

Zea_mays2

Clones by site

Clones by phase

Sequence size

Contig totals

namecount(*)sum(length)min(length)max(length)clone48680220546690478466

Contigs by Chromosome

Total Genes

count(*)12632

Genes by Analysis

programngenefgenesh12632

Genes by type

typecount(*)12632

Number of Transcripts, Number of Translations

count(*)12632count(*)12632

htg_phase count(*)
0 513
3 3617

name count(*) sum(length) min(length) max(length)
chromosome 22 372093005 103307 43249587
clone 4130 576159227 713 354587

chrnum count(*) sum(length)
0 10 1146791
1 442 63976768
2 439 59569338
3 352 48614722
4 363 49501890
5 325 44099447
6 336 44691077
7 365 48966432
8 345 48604168
9 270 37652003
10 297 52948295
11 289 39463406
12 297 36924890

count(*)
121153

program ngene
Submitter_tRNA_Annotation 171
SubmitterGeneAnnotation 62230
tigr 58752

type count(*)
known 62401
TE-like 14196
tigr 44556

count()
124493
count()
124322

count()
494876
name min(seq_region_end-seq_region_start+1) avg(seq_region_end-seq_region_start+1) max(seq_region_end-seq_region_start+1) count()
chromosome 1 349.3509 15363 261415
clone 4 282.9544 17928 233461

name min(seq_region_end-seq_region_start+1) avg(seq_region_end-seq_region_start+1) max(seq_region_end-seq_region_start+1) count(*)
chromosome 1 349.3509 15363 261415
clone 4 282.9544 17928 233461

ensembl_object_type count(*)
Transcript 212978
Gene 228049
Translation 74376

db_name xcount
SWISSPROT 664
GO 1210
EGAD 10
GP 4710
PF 1525
PIR 1209
TIGR_FN 120844
TIGR_TU 58752
TIGR_MODEL 62149
TIGR 446
TIGR_LOCUS 126310
GRAMENE_OLD 52139
Interpro 3537

logic_name gff_feature gff_source program npt
fgenesh prediction FgenesH:Monocot fgenesh 56170

mtype logic_name program mcount hcount
est Rice_rflp_marker NULL 6612 6614
tos17 Rice_tos17_insert NULL 16478 16856
microsatellite Rice_SSR NULL 2660 3126

logic_name program ccount hcount
Rice_TE NULL 57 11619

min(name) sum(asm_end-asm_start)
1 214765510
10 114503652
2 187580374
3 183721938
4 199417804
5 171048909
6 116031455
7 121458656
8 127352791
9 100151268
? 17760245
UNKNOWN 242192040
1 1795984642

name count(*) sum(length) min(length) max(length)
chromosome 12 1795985408 17760256 242192384
fpc 766 1795985408 36864 19161088

count(*)
0

count()
0
count()
0

count(*)
0

mtype logic_name program mcount hcount
microsatellite Maize_marker NULL 19232 67243

name count(*) sum(length) min(length) max(length)
clone 486 80220546 690 478466

count(*)
12632

program ngene
fgenesh 12632

type count(*)
12632

count()
12632
count()
12632

count()
50699
name min(seq_region_end-seq_region_start+1) avg(seq_region_end-seq_region_start+1) max(seq_region_end-seq_region_start+1) count()
clone 1 484.5918 5670 50699

name min(seq_region_end-seq_region_start+1) avg(seq_region_end-seq_region_start+1) max(seq_region_end-seq_region_start+1) count(*)
clone 1 484.5918 5670 50699

exons count(*)
1 9171
2 11440
3 8566
4 6452
5 4811
6 3578
7 2349
8 1751
9 1157
10 729
11 592
12 468
13 354
14 239
15 166
16 107
17 117
18 68
19 67
20 44
21 12
22 36
23 8
24 4
25 16
28 4
30 4
31 12
32 8
38 4
41 4
50 4

ensembl_object_type count(*)
Translation 15351

db_name xcount
GO 450
Interpro 957

min(name) sum(asm_end-asm_start)
1 30431172
2 19703100
3 23467471
4 18581833
5 26989310
1 119172886

name count(*) sum(length) min(length) max(length)
chromosome 5 119186497 18585042 30432563
contig 1611 135187985 444 1874423

count(*)
29993

program ngene
NULL 29993

type count(*)
Gene 26207
Pseudogene 3786

count()
32739
count()
32739

count()
156461
name min(seq_region_end-seq_region_start+1) avg(seq_region_end-seq_region_start+1) max(seq_region_end-seq_region_start+1) count()
chromosome 1 327.9428 15195 156461