ChromoView - clone / Assembly sequencing status

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

TPF

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# 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
bI548A10
BX548169.4
finished
12 PigI-35B1
mhc_class_III
bI35B1
AL773591.7
finished
13 PigI-711D2
mhc_class_III
bI711D2
AL773559.16
finished
14 PigI-707F1
mhc_class_III
bI707F1
AL773527.8
finished
15 PigI-514B12
mhc_class_III
bI514B12
AL773560.9
finished
16 PigI-446E4
mhc_class_III
bI446E4
BX322232.4
finished
17 PigI-649D6
mhc_class_III
bI649D6
AL773562.15
finished
18 PigI-339A5
mhc_class_III
bI339A5
AL773521.18
finished
  GAP (type-4) length 3000000 bps    
20 PigI-43B6
mhc_class_II
bI43B6
BX323846.2
finished
21 PigI-591C4
mhc_class_II
bI591C4
BX088590.7
finished
22 PigI-554F3
mhc_class_II
bI554F3
BX323833.4
finished
23 PigI-1044B7
mhc_class_II
bI1044B7
BX324144.4
finished
24 PigI-279G2
mhc_class_II
bI279G2
BX640585.2
finished

AGP

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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

Component Sanger::HumPub::ChromoView failed to execute

Statistics

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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, 17 Apr 2015 14:55
2 5 AJ131112.2 1 98,106 1 Double 3-prime join to 'AJ131112.2' Fri, 17 Apr 2015 14:55

Dovetails

# rank accession status length date
1 3 AJ251829.1 unfinished 228 Fri, 17 Apr 2015 14:55
2 4 AJ131112.2 unfinished 8,349 Fri, 17 Apr 2015 14:55
3 9 AB113354.2 unfinished 34,969 Fri, 17 Apr 2015 14:55
4 10 AJ251914.1 unfinished 1,852 Fri, 17 Apr 2015 14:55

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Other links

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