ChromoView - clone / Assembly sequencing status

Pig: Sub region Pig_MHC (TPF updated: 2006-02-15)

TPF

# Clone ext/Contig Clone int Acc/Fin
1 PigI-649H10
mhc_class_I
bI649H10
AB158486.1
finished
2 PigI-792A7
mhc_class_I
bI792A7
AB158487.1
finished
3 PigI-207G8
mhc_class_I
bI207G8
AJ251829.1
finished
4 PigI-490B10
mhc_class_I
bI490B10
AJ131112.2
finished
5 PigI-771G4
mhc_class_I
bI771G4
AB158488.1
finished
6 PigI-1111D10
mhc_class_I
bI1111D10
AB113357.1
finished
7 PigI-1051H9
mhc_class_I
bI1051H9
AB113356.1
finished
8 PigI-353A11
mhc_class_I
bI353A11
AB113355.2
finished
9 PigI-499E6
mhc_class_I
bI499E6
AB113354.2
finished
10 PigI-493A6
mhc_class_I
bI493A6
AJ251914.1
finished
11 PigI-548A10
mhc_class_III
Cl/Pr bI548A10/bS548A10 swap
EPN details
BX548169.4
finished
12 PigI-35B1
mhc_class_III
Cl/Pr bI35B1/bS35B1 swap
EPN details
AL773591.7
finished
13 PigI-711D2
mhc_class_III
Cl/Pr bI711D2/bS711D2 swap
EPN details
AL773559.16
finished
14 PigI-707F1
mhc_class_III
Cl/Pr bI707F1/bS707F1 swap
EPN details
AL773527.8
finished
15 PigI-514B12
mhc_class_III
Cl/Pr bI514B12/bS514B12 swap
EPN details
AL773560.9
finished
16 PigI-446E4
mhc_class_III
Cl/Pr bI446E4/bS446E4 swap
EPN details
BX322232.4
finished
17 PigI-649D6
mhc_class_III
Cl/Pr bI649D6/bS649D6 swap
EPN details
AL773562.15
finished
18 PigI-339A5
mhc_class_III
Cl/Pr bI339A5/bS339A5 swap
EPN details
AL773521.18
finished
  GAP (type-4) length 3000000 bps    
20 PigI-43B6
mhc_class_II
Cl/Pr bI43B6/bS43B6 swap
EPN details
BX323846.2
finished
21 PigI-591C4
mhc_class_II
Cl/Pr bI591C4/bS591C4 swap
EPN details
BX088590.7
finished
22 PigI-554F3
mhc_class_II
Cl/Pr bI554F3/bS554F3 swap
EPN details
BX323833.4
finished
23 PigI-1044B7
mhc_class_II
Cl/Pr bI1044B7/bS1044B7 swap
EPN details
BX324144.4
finished
24 PigI-279G2
mhc_class_II
Cl/Pr bI279G2/bS279G2 swap
EPN details
BX640585.2
finished

AGP

AGP_S AGP_E Rank Status Acc.ver Clone_S Clone_E Str
1 94152 1 FClick to retrieve finished assembled sequence in green bar: rank(s) 1 - 2 AB158486.1 1 94152 +
94153 182504 2 FClick to retrieve finished assembled sequence in green bar: rank(s) 1 - 2 AB158487.1 1 88352 +
182505 334291 3 F AJ251829.1
Double 5-prime join to 'AJ251829.1'
425 152211 -
334292 339291 4 N 5000 Bad overlap - double 5 prime join    
339292 437397 5 F AJ131112.2
Double 3-prime join to 'AJ131112.2'
1 98106 +
437398 442397 6 N 5000 Bad overlap - double 3 prime join    
442398 589783 7 FClick to retrieve finished assembled sequence in green bar: rank(s) 7 - 11 AB158488.1 1 147386 +
589784 694750 8 FClick to retrieve finished assembled sequence in green bar: rank(s) 7 - 11 AB113357.1 9409 114375 +
694751 755624 9 FClick to retrieve finished assembled sequence in green bar: rank(s) 7 - 11 AB113356.1 72837 133710 +
755625 858705 10 FClick to retrieve finished assembled sequence in green bar: rank(s) 7 - 11 AB113355.2 41368 144448 -
858706 978199 11 FClick to retrieve finished assembled sequence in green bar: rank(s) 7 - 11 AB113354.2 35256 154749 -
978200 1108919 12 F AJ251914.1
Double 5-prime join to 'AJ251914.1'
27344 158063 -
1108920 1113919 13 N 5000 Bad overlap - double 5 prime join    
1113920 1215167 14 FClick to retrieve finished assembled sequence in green bar: rank(s) 14 - 21 BX548169.4 1 101248 -
1215168 1331571 15 FClick to retrieve finished assembled sequence in green bar: rank(s) 14 - 21 AL773591.7 1 116404 -
1331572 1362141 16 FClick to retrieve finished assembled sequence in green bar: rank(s) 14 - 21 AL773559.16 1 30570 -
1362142 1497427 17 FClick to retrieve finished assembled sequence in green bar: rank(s) 14 - 21 AL773527.8 1 135286 -
1497428 1602840 18 FClick to retrieve finished assembled sequence in green bar: rank(s) 14 - 21 AL773560.9 1 105413 -
1602841 1604834 19 FClick to retrieve finished assembled sequence in green bar: rank(s) 14 - 21 BX322232.4 1 1994 -
1604835 1730099 20 FClick to retrieve finished assembled sequence in green bar: rank(s) 14 - 21 AL773562.15 1 125265 -
1730100 1800653 21 FClick to retrieve finished assembled sequence in green bar: rank(s) 14 - 21 AL773521.18 1 70554 -
1800654 4800653 22 N 3000000 Centromere no
4800654 4880802 23 FClick to retrieve finished assembled sequence in green bar: rank(s) 23 - 27 BX323846.2 1 80149 -
4880803 5044592 24 FClick to retrieve finished assembled sequence in green bar: rank(s) 23 - 27 BX088590.7 1 163790 -
5044593 5164075 25 FClick to retrieve finished assembled sequence in green bar: rank(s) 23 - 27 BX323833.4 1 119483 -
5164076 5286385 26 FClick to retrieve finished assembled sequence in green bar: rank(s) 23 - 27 BX324144.4 1 122310 -
5286386 5380480 27 FClick to retrieve finished assembled sequence in green bar: rank(s) 23 - 27 BX640585.2 1 94095 -

Details

# Clone ext/Contig Clone int Status/Date Acc/Fin Length Library OL Pos OL Qual OL details Cert
1 PigI-649H10
mhc_class_I
bI649H10
-
-
AB158486.1
finished
156044 SBAB bI Clones 3' / 5'
94152 / 1
- / -
61893
0
Identified
2008-11-28
find_overl...
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2 PigI-792A7
mhc_class_I
bI792A7
-
-
AB158487.1
finished
143480 SBAB bI Clones 3' / 5'
88352 / 1
- / -
55129
0
Identified
2008-11-28
find_overl...
humpub
 
3 PigI-207G8
mhc_class_I
bI207G8
-
-
AJ251829.1
finished
152211 SBAB bI Clones 5' / 3'
425 / 146433
228 / 8349
199
22.11
Identified
2008-11-12
find_overl...
humpub
 
4 PigI-490B10
mhc_class_I
bI490B10
-
-
AJ131112.2
finished
154782 SBAB bI Clones 3' / 5'
98106 / 1
- / -
56677
0
Identified
2008-11-28
find_overl...
humpub
 
5 PigI-771G4
mhc_class_I
bI771G4
-
-
AB158488.1
finished
147386 SBAB bI Clones 3' / 5'
147386 / 9409
- / -
9408
0
Identified
2008-11-28
find_overl...
humpub
 
6 PigI-1111D10
mhc_class_I
bI1111D10
-
-
AB113357.1
finished
114375 SBAB bI Clones 3' / 5'
114375 / 72837
- / -
72838
0
Identified
2008-11-12
find_overl...
humpub
 
7 PigI-1051H9
mhc_class_I
bI1051H9
-
-
AB113356.1
finished
146382 SBAB bI Clones 3' / 3'
133710 / 144448
- / -
12672
0
Identified
2008-11-12
find_overl...
humpub
 
8 PigI-353A11
mhc_class_I
bI353A11
-
-
AB113355.2
finished
144448 SBAB bI Clones 5' / 3'
41368 / 154749
- / -
41375
0.07
Identified
2008-11-12
find_overl...
humpub
 
9 PigI-499E6
mhc_class_I
bI499E6
-
-
AB113354.2
finished
154749 SBAB bI Clones 5' / 5'
35256 / 1853
34969 / 1852
293
12.63
Identified
2008-11-12
find_overl...
humpub
 
10 PigI-493A6
mhc_class_I
bI493A6
-
-
AJ251914.1
finished
158063 SBAB bI Clones 5' / 3'
27344 / 101248
- / -
27352
0.03
Identified
2008-11-28
find_overl...
humpub
 
11 PigI-548A10
mhc_class_III
Cl/Pr bI548A10/bS548A10 swap
EPN details
Submitted to EMBL
18-MAY-07
BX548169.4
finished
101248 SBAB bI Clones 5' / 3'
1 / 116404
- / -
2000
0
Identified
2008-11-28
find_overl...
humpub
 
12 PigI-35B1
mhc_class_III
Cl/Pr bI35B1/bS35B1 swap
EPN details
Submitted to EMBL
05-JUN-07
AL773591.7
finished
118404 SBAB bI Clones 5' / 3'
1 / 30570
- / -
2000
0
Identified
2008-11-28
find_overl...
humpub
 
13 PigI-711D2
mhc_class_III
Cl/Pr bI711D2/bS711D2 swap
EPN details
Submitted to EMBL
17-MAY-07
AL773559.16
finished
32570 SBAB bI Clones 5' / 3'
1 / 135286
- / -
2000
0
Identified
2008-11-28
find_overl...
humpub
 
14 PigI-707F1
mhc_class_III
Cl/Pr bI707F1/bS707F1 swap
EPN details
Submitted to EMBL
07-JUN-07
AL773527.8
finished
137286 SBAB bI Clones 5' / 3'
1 / 105413
- / -
2000
0
Identified
2008-11-28
find_overl...
humpub
 
15 PigI-514B12
mhc_class_III
Cl/Pr bI514B12/bS514B12 swap
EPN details
Submitted to EMBL
18-MAY-07
AL773560.9
finished
107413 SBAB bI Clones 5' / 3'
1 / 1994
- / -
2007
0
Identified
2008-11-28
find_overl...
humpub
 
16 PigI-446E4
mhc_class_III
Cl/Pr bI446E4/bS446E4 swap
EPN details
Submitted to EMBL
17-MAY-07
BX322232.4
finished
4001 SBAB bI Clones 5' / 3'
1 / 125265
- / -
2000
0
Identified
2008-11-28
find_overl...
humpub
 
17 PigI-649D6
mhc_class_III
Cl/Pr bI649D6/bS649D6 swap
EPN details
Submitted to EMBL
17-MAY-07
AL773562.15
finished
127265 SBAB bI Clones 5' / 3'
1 / 70554
- / -
2000
0
Identified
2008-11-28
find_overl...
humpub
 
18 PigI-339A5
mhc_class_III
Cl/Pr bI339A5/bS339A5 swap
EPN details
Submitted to EMBL
17-MAY-07
AL773521.18
finished
72554 SBAB bI Clones        
  GAP (type-4) length 3000000 bps                  
20 PigI-43B6
mhc_class_II
Cl/Pr bI43B6/bS43B6 swap
EPN details
Submitted to EMBL
17-MAY-07
BX323846.2
finished
80149 SBAB bI Clones 5' / 3'
1 / 163790
- / -
2000
0
Identified
2008-11-28
find_overl...
humpub
 
21 PigI-591C4
mhc_class_II
Cl/Pr bI591C4/bS591C4 swap
EPN details
Submitted to EMBL
17-MAY-07
BX088590.7
finished
165790 SBAB bI Clones 5' / 3'
1 / 119483
- / -
2000
0
Identified
2008-11-28
find_overl...
humpub
 
22 PigI-554F3
mhc_class_II
Cl/Pr bI554F3/bS554F3 swap
EPN details
Submitted to EMBL
17-MAY-07
BX323833.4
finished
121483 SBAB bI Clones 5' / 3'
1 / 122310
- / -
2000
0
Identified
2008-11-28
find_overl...
humpub
 
23 PigI-1044B7
mhc_class_II
Cl/Pr bI1044B7/bS1044B7 swap
EPN details
Submitted to EMBL
17-MAY-07
BX324144.4
finished
124310 SBAB bI Clones 5' / 3'
1 / 94095
- / -
2000
0
Identified
2008-11-28
find_overl...
humpub
 
24 PigI-279G2
mhc_class_II
Cl/Pr bI279G2/bS279G2 swap
EPN details
Submitted to EMBL
17-MAY-07
BX640585.2
finished
96095 SBAB bI Clones        

Statistics

Clone Summary

Number of gaps
1
Gap types
type-4
1
Total clones
23
Clone HTGS Phases
finished
23
Number of clones w/o accession
0

Overlap Summary

Total overlap length of fin clones
359,843
Total finished length of fin clones w/ overlap
2,760,488
Total finished length of fin clones w/o overlap
2,400,645
Total overlap length of fin+unfin clones
359,843
Total finished length of fin+unfin clones w/ overlap
2,760,488
Total finished length of fin+unfin clones w/o overlap
2,400,645

AGP errors

# rank accession seq_start seq_end strand error date
1 3 AJ251829.1 425 152,211 -1 Double 5-prime join to 'AJ251829.1' Fri, 25 Apr 2014 01:33
2 5 AJ131112.2 1 98,106 1 Double 3-prime join to 'AJ131112.2' Fri, 25 Apr 2014 01:33

Dovetails

# rank accession status length date
1 3 AJ251829.1 unfinished 228 Fri, 25 Apr 2014 01:33
2 4 AJ131112.2 unfinished 8,349 Fri, 25 Apr 2014 01:33
3 9 AB113354.2 unfinished 34,969 Fri, 25 Apr 2014 01:33
4 10 AJ251914.1 unfinished 1,852 Fri, 25 Apr 2014 01:33

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Other links

* quick link - http://q.sanger.ac.uk/4kr484gf