ChromoView - clone / Assembly sequencing status

Pig: Chromosome U (TPF updated: 2012-08-29)

TPF

# Clone ext/Contig Clone int Acc/Fin
1 PigE-29D16
ctg20927
bT29D16
EPN details

-
  GAP (type-3) length unknown    
3 PigE-38F3
ctg20928
bT38F3
EPN details

-
  GAP (type-2) length unknown    
  GAP (type-3) length unknown    
6 PigI-598C9
ctg30006
bI598C9
EPN details
FP085608.1
unfinished
7 PigI-437A9
ctg30006
bI437A9
EPN details
FP101904.2
unfinished
8 PigI-148B7
ctg30006
bI148B7
EPN details
FP236246.1
unfinished
9 PigI-521H5
ctg30006
bI521H5
EPN details
FP102388.1
unfinished
10 PigI-491F11
ctg30006
bI491F11
EPN details
FP085361.1
unfinished
11 PigI-759D9
ctg30006
bI759D9
EPN details
FP102766.1
unfinished
12 PigI-644C12
ctg30006
bI644C12
EPN details
FP085609.1
unfinished
13 PigI-398E11
ctg30006
bI398E11
EPN details
FP085360.1
unfinished
14 PigI-131C8
ctg30006
bI131C8
EPN details

-
15 PigI-657F11
ctg30006
bI657F11
EPN details
FP085426.1
unfinished
16 PigI-436E4
ctg30006
bI436E4
EPN details
FP102387.1
unfinished
  GAP (type-3) length unknown    
18 CH242-74M3
ctg30008
bE74M3
EPN details
FP015876.3
finished
  GAP (type-3) length unknown    
20 CH242-155F24
ctg30009
bE155F24
EPN details
FP312877.2
unfinished
21 CH242-3K19
ctg30009
bE3K19
EPN details
CU571362.2
unfinished
22 CH242-171F7
ctg30009
bE171F7
EPN details
CU856325.3
unfinished
23 CH242-506D3
ctg30009
bE506D3
EPN details
FP236739.3
unfinished
  GAP (type-3) length unknown    

AGP

AGP_S AGP_E Rank Status Acc.ver Clone_S Clone_E Str
1 50000 1 N 50000 clone no
50001 100000 2 N 50000 contig no
100001 150000 3 N 50000 clone no
150001 200000 4 N 50000 contig yes
200001 250000 5 N 50000 contig no
250001 300000 6 N 50000 clone no
300001 350000 7 N 50000 clone yes
350001 400000 8 N 50000 clone yes
400001 450000 9 N 50000 clone yes
450001 500000 10 N 50000 clone yes
500001 550000 11 N 50000 clone yes
550001 600000 12 N 50000 clone yes
600001 650000 13 N 50000 clone yes
650001 700000 14 N 50000 clone yes
700001 750000 15 N 50000 clone yes
750001 800000 16 N 50000 clone no
800001 850000 17 N 50000 contig no
850001 1019238 18 FClick to retrieve finished assembled sequence in green bar: rank(s) 18 - 18 FP015876.3 1 169238 +
1019239 1069238 19 N 50000 contig no
1069239 1119238 20 N 50000 clone no
1119239 1169238 21 N 50000 clone yes
1169239 1219238 22 N 50000 clone yes
1219239 1269238 23 N 50000 clone no
1269239 1319238 24 N 50000 contig no

Details

# Clone ext/Contig Clone int Status/Date Acc/Fin Length Library OL Pos OL Qual OL details Cert
1 PigE-29D16
ctg20927
bT29D16
EPN details
Shotgun complete
09-JUN-10

-
- PigE        
  GAP (type-3) length unknown                  
3 PigE-38F3
ctg20928
bT38F3
EPN details
Manually Improved
23-JUL-12

-
- PigE        
  GAP (type-2) length unknown                  
  GAP (type-3) length unknown                  
6 PigI-598C9
ctg30006
bI598C9
EPN details
Shotgun complete
01-SEP-09
FP085608.1
unfinished
108124 SBAB bI Clones 5' / 5'
1 / 3277
- / -
3320
5.12
Identified
2009-02-27
find_overl...
humpub
 
7 PigI-437A9
ctg30006
bI437A9
EPN details
Shotgun complete
01-SEP-09
FP101904.2
unfinished
98057 SBAB bI Clones 3' / 3'
95268 / 43551
469 / 2440
2330
14.44
Identified
2009-02-27
find_overl...
humpub
 
8 PigI-148B7
ctg30006
bI148B7
EPN details
Shotgun complete
01-SEP-09
FP236246.1
unfinished
45991 SBAB bI Clones 3' / 5'
45991 / 5939
- / 3759
2182
0.6
Identified
2009-02-27
find_overl...
humpub
 
9 PigI-521H5
ctg30006
bI521H5
EPN details
Shotgun complete
01-SEP-09
FP102388.1
unfinished
47536 SBAB bI Clones 5' / 5'
20566 / 1220
20565 / 84
1136
0.27
Identified
2009-02-27
find_overl...
humpub
 
10 PigI-491F11
ctg30006
bI491F11
EPN details
Shotgun complete
01-SEP-09
FP085361.1
unfinished
137761 SBAB bI Clones 3' / 3'
76503 / 106850
61258 / -
2572
2.71
Identified
2009-03-10
find_overl...
humpub
 
11 PigI-759D9
ctg30006
bI759D9
EPN details
Shotgun complete
01-SEP-09
FP102766.1
unfinished
109421 SBAB bI Clones 3' / 5'
70221 / 2498
39139 / 2497
62
9.84
Identified
2009-02-27
find_overl...
humpub
 
12 PigI-644C12
ctg30006
bI644C12
EPN details
Shotgun complete
01-SEP-09
FP085609.1
unfinished
110840 SBAB bI Clones 5' / 3'
1 / 73249
- / 59797
639
3.13
Identified
2009-02-27
find_overl...
humpub
 
13 PigI-398E11
ctg30006
bI398E11
EPN details
Shotgun complete
01-SEP-09
FP085360.1
unfinished
133685 SBAB bI Clones        
14 PigI-131C8
ctg30006
bI131C8
EPN details
Shotgun complete
01-SEP-09

-
- SBAB bI Clones        
15 PigI-657F11
ctg30006
bI657F11
EPN details
Shotgun complete
01-SEP-09
FP085426.1
unfinished
58065 SBAB bI Clones 3' / 3'
58065 / 51807
- / 38844
3318
7.75
Identified
2009-02-27
find_overl...
humpub
 
16 PigI-436E4
ctg30006
bI436E4
EPN details
Shotgun complete
01-SEP-09
FP102387.1
unfinished
93936 SBAB bI Clones        
  GAP (type-3) length unknown                  
18 CH242-74M3
ctg30008
bE74M3
EPN details
Analysed
15-MAY-09
FP015876.3
finished
169238 CHORI-242        
  GAP (type-3) length unknown                  
20 CH242-155F24
ctg30009
bE155F24
EPN details
Auto-prefinishing complete
10-AUG-09
FP312877.2
unfinished
161649 CHORI-242 3' / 5'
161649 / 19490
- / -
19491
0.03
Identified
2009-08-10
find_overl...
humpub
 
21 CH242-3K19
ctg30009
bE3K19
EPN details
Auto-prefinishing complete
15-JUL-08
CU571362.2
unfinished
160516 CHORI-242 3' / 3'
160516 / 144154
- / 33997
7565
0.01
Identified
2009-05-17
find_overl...
humpub
 
22 CH242-171F7
ctg30009
bE171F7
EPN details
Auto-prefinishing complete
15-SEP-08
CU856325.3
unfinished
185715 CHORI-242 3' / 5'
172821 / 1
6900 / -
5995
0.09
Identified
2009-07-18
find_overl...
humpub
 
23 CH242-506D3
ctg30009
bE506D3
EPN details
Auto-prefinishing complete
15-JUL-09
FP236739.3
unfinished
99051 CHORI-242        
  GAP (type-3) length unknown                  

Statistics

Clone Summary

Number of gaps
6
Gap types
type-2
1
type-3
5
Total clones
18
Clone HTGS Phases
finished
1
unfinished
14
Number of clones w/o accession
3
Clones w/o htgs phase
3
Non-htgs clonenames
PigE-29D16 (bT29D16), PigE-38F3 (bT38F3), PigI-131C8 (bI131C8)

Overlap Summary

Total overlap length of fin clones
0
Total finished length of fin clones w/ overlap
169,238
Total finished length of fin clones w/o overlap
169,238
Total overlap length of fin+unfin clones
48,610
Total finished length of fin+unfin clones w/ overlap
1,719,585
Total finished length of fin+unfin clones w/o overlap
1,670,975

Dovetails

# rank accession status length date
1 7 FP101904.2 unfinished 469 Thu, 24 Jul 2014 01:53
2 8 FP236246.1 unfinished 2,440 Thu, 24 Jul 2014 01:53
3 9 FP102388.1 unfinished 3,759 Thu, 24 Jul 2014 01:53
4 9 FP102388.1 unfinished 20,565 Thu, 24 Jul 2014 01:53
5 10 FP085361.1 unfinished 84 Thu, 24 Jul 2014 01:53
6 10 FP085361.1 unfinished 61,258 Thu, 24 Jul 2014 01:53
7 11 FP102766.1 unfinished 39,139 Thu, 24 Jul 2014 01:53
8 12 FP085609.1 unfinished 2,497 Thu, 24 Jul 2014 01:53
9 13 FP085360.1 unfinished 59,797 Thu, 24 Jul 2014 01:53
10 16 FP102387.1 unfinished 38,844 Thu, 24 Jul 2014 01:53
11 22 CU856325.3 unfinished 33,997 Thu, 24 Jul 2014 01:53
12 22 CU856325.3 unfinished 6,900 Thu, 24 Jul 2014 01:53

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Other links

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