ChromoView - clone / Assembly sequencing status

Human: Sub region GRC__HUMAN__ALT_REF_LOCI_1__11 (TPF updated: 2014-07-24)

TPF

# Clone ext/Contig Clone int Acc/Fin
1 RP11-47K5
Hschr11_1_ctg1_1
CONTAINER
bA47K5
EPN details
AC009638.9
finished
2 ABC10-45523400D1
Hschr11_1_ctg1_1
CONTAINED
f10A45523400D1
AC203610.2
finished
1 RP11-47K5
Hschr11_1_ctg1_1
CONTAINER
bA47K5
EPN details
AC009638.9
finished
  GAP (type-3) length unknown    
4 RP11-444K7
HG142_HG150_NOVEL_test
bA444K7
EPN details
AC022882.5
finished
5 ABC9-45432900N15
HG142_HG150_NOVEL_test
f9A45432900N15
AC208786.2
finished
  GAP (type-3) length unknown    
7 ABC7-42515900E16
HG151_NOVEL_test
f7A42515900E16
AC213223.1
finished
8 RP11-100N3
HG151_NOVEL_test
bA100N3
EPN details
AP001803.4
finished
  GAP (type-3) length unknown    
10 RP11-410I24
Hschr11_1_ctg2
bA410I24
EPN details
AP003050.4
finished
11 ABC27-1383D18
Hschr11_1_ctg2
f27A1383D18
AC240134.3
finished
  GAP (type-3) length unknown    
13 ABC14-50997500E11
Hschr11_1_ctg3
f14A50997500E11
AC225595.1
finished
14 CMB9-65A1
Hschr11_1_ctg3
cmb9E65A1
AP005140.4
finished
  GAP (type-3) length unknown    
16 RP11-494M8
Hschr11_1_ctg5
CONTAINER
bA494M8
EPN details
AC044810.7
finished
17 ABC10-1605870K7
Hschr11_1_ctg5
CONTAINED
f10A1605870K7
AC209551.4
finished
16 RP11-494M8
Hschr11_1_ctg5
CONTAINER
bA494M8
EPN details
AC044810.7
finished
  GAP (type-3) length unknown    
19 RP13-25N22
Hschr11_1_ctg6
CONTAINER
bB25N22
EPN details
AP006285.2
finished
20 ABC10-44565900B4
Hschr11_1_ctg6
CONTAINED
f10A44565900B4
AC211344.3
finished
19 RP13-25N22
Hschr11_1_ctg6
CONTAINER
bB25N22
EPN details
AP006285.2
finished
  GAP (type-3) length unknown    
22 RP11-19N21
Hschr11_1_ctg7
CONTAINER
bA19N21
AC013791.9
finished
23
Hschr11_1_ctg7
CONTAINED
KF455305
KF455305.1
finished
22 RP11-19N21
Hschr11_1_ctg7
CONTAINER
bA19N21
AC013791.9
finished
24
Hschr11_1_ctg7
CONTAINED
KF455306
KF455306.1
finished
22 RP11-19N21
Hschr11_1_ctg7
CONTAINER
bA19N21
AC013791.9
finished
25 HSAC001228
Hschr11_1_ctg7
HSAC001228
AC001228.1
finished
  GAP (type-3) length unknown    
27 RP13-46H24
Hschr11_1_ctg8
bB46H24
EPN details
AC137894.5
finished
28 CTD-2647G13
Hschr11_1_ctg8
bK2647G13
AC138374.2
finished

AGP

AGP_S AGP_E Rank Status Acc.ver Clone_S Clone_E Str
1 34263 1 FClick to retrieve finished assembled sequence in green bar: rank(s) 1 - 3 AC009638.9 1 34263 +
34264 75179 2 FClick to retrieve finished assembled sequence in green bar: rank(s) 1 - 3 AC203610.2 1 40916 +
75180 163343 3 FClick to retrieve finished assembled sequence in green bar: rank(s) 1 - 3 AC009638.9 69447 157610 +
163344 213343 4 N 50000 contig no
213344 380293 5 FClick to retrieve finished assembled sequence in green bar: rank(s) 5 - 6 AC022882.5 1 166950 +
380294 414341 6 FClick to retrieve finished assembled sequence in green bar: rank(s) 5 - 6 AC208786.2 1 34048 +
414342 464341 7 N 50000 contig no
464342 498234 8 FClick to retrieve finished assembled sequence in green bar: rank(s) 8 - 9 AC213223.1 1 33893 -
498235 655750 9 FClick to retrieve finished assembled sequence in green bar: rank(s) 8 - 9 AP001803.4 1857 159372 +
655751 705750 10 N 50000 contig no
705751 858465 11 FClick to retrieve finished assembled sequence in green bar: rank(s) 11 - 12 AP003050.4 1 152715 +
858466 891919 12 FClick to retrieve finished assembled sequence in green bar: rank(s) 11 - 12 AC240134.3 1 33454 -
891920 941919 13 N 50000 contig no
941920 979328 14 FClick to retrieve finished assembled sequence in green bar: rank(s) 14 - 15 AC225595.1 1 37409 -
979329 1037493 15 FClick to retrieve finished assembled sequence in green bar: rank(s) 14 - 15 AP005140.4 54437 112601 +
1037494 1087493 16 N 50000 contig no
1087494 1145597 17 FClick to retrieve finished assembled sequence in green bar: rank(s) 17 - 19 AC044810.7 1 58104 +
1145598 1188497 18 FClick to retrieve finished assembled sequence in green bar: rank(s) 17 - 19 AC209551.4 1 42900 -
1188498 1292423 19 FClick to retrieve finished assembled sequence in green bar: rank(s) 17 - 19 AC044810.7 90372 194297 +
1292424 1342423 20 N 50000 contig no
1342424 1367933 21 FClick to retrieve finished assembled sequence in green bar: rank(s) 21 - 23 AP006285.2 1 25510 +
1367934 1405060 22 FClick to retrieve finished assembled sequence in green bar: rank(s) 21 - 23 AC211344.3 1 37127 +
1405061 1538400 23 FClick to retrieve finished assembled sequence in green bar: rank(s) 21 - 23 AP006285.2 56928 190267 +
1538401 1588400 24 N 50000 contig no
1588401 1636407 25 FClick to retrieve finished assembled sequence in green bar: rank(s) 25 - 30 AC013791.9 126563 174569 -
1636408 1636785 26 FClick to retrieve finished assembled sequence in green bar: rank(s) 25 - 30 KF455305.1 1 378 -
1636786 1640380 27 FClick to retrieve finished assembled sequence in green bar: rank(s) 25 - 30 AC013791.9 122590 126184 -
1640381 1640767 28 FClick to retrieve finished assembled sequence in green bar: rank(s) 25 - 30 KF455306.1 1 387 -
1640768 1641041 29 FClick to retrieve finished assembled sequence in green bar: rank(s) 25 - 30 AC013791.9 121929 122202 -
1641042 1885295 30 FClick to retrieve finished assembled sequence in green bar: rank(s) 25 - 30 AC001228.1 1 244254 +
1885296 1935295 31 N 50000 contig no
1935296 2100295 32 FClick to retrieve finished assembled sequence in green bar: rank(s) 32 - 33 AC137894.5 1 165000 +
2100296 2237475 33 FClick to retrieve finished assembled sequence in green bar: rank(s) 32 - 33 AC138374.2 59245 196424 +

Details

# Clone ext/Contig Clone int Status/Date Acc/Fin Length Library OL Pos OL Qual OL details Cert
1 RP11-47K5
Hschr11_1_ctg1_1
CONTAINER
bA47K5
EPN details
Externally Finished
21-JAN-13
AC009638.9
finished
157610 RPCI-11.1 3' / 5'
34263 / 1
88164 / -
40916
16.41
Identified
2014-07-24
fetch_ncbi...
humpub
Certificate approved
2 ABC10-45523400D1
Hschr11_1_ctg1_1
CONTAINED
f10A45523400D1
-
-
AC203610.2
finished
40916 ABC10 3' / 5'
40916 / 69447
- / 34263
40916
16.41
Identified
2014-07-24
fetch_ncbi...
humpub
Certificate approved
1 RP11-47K5
Hschr11_1_ctg1_1
CONTAINER
bA47K5
EPN details
Externally Finished
21-JAN-13
AC009638.9
finished
157610 RPCI-11.1        
  GAP (type-3) length unknown                  
4 RP11-444K7
HG142_HG150_NOVEL_test
bA444K7
EPN details
Externally Finished
21-JAN-13
AC022882.5
finished
174469 RPCI-11.2 3' / 5'
166950 / 1
- / -
7519
0.08
Identified
2014-07-24
fetch_ncbi...
humpub
 
5 ABC9-45432900N15
HG142_HG150_NOVEL_test
f9A45432900N15
-
-
AC208786.2
finished
34048 ABC9        
  GAP (type-3) length unknown                  
7 ABC7-42515900E16
HG151_NOVEL_test
f7A42515900E16
-
-
AC213223.1
finished
33893 ABC7 5' / 5'
1 / 1857
- / -
1856
0.27
Identified
2014-07-24
fetch_ncbi...
humpub
 
8 RP11-100N3
HG151_NOVEL_test
bA100N3
EPN details
Externally Finished
21-OCT-13
AP001803.4
finished
159372 RPCI-11.1        
  GAP (type-3) length unknown                  
10 RP11-410I24
Hschr11_1_ctg2
bA410I24
EPN details
Externally Finished
21-JAN-13
AP003050.4
finished
152715 RPCI-11.2 3' / 3'
152715 / 33454
- / -
7582
0.3
Identified
2014-07-24
fetch_ncbi...
humpub
 
11 ABC27-1383D18
Hschr11_1_ctg2
f27A1383D18
-
-
AC240134.3
finished
41046 ABC27        
  GAP (type-3) length unknown                  
13 ABC14-50997500E11
Hschr11_1_ctg3
f14A50997500E11
-
-
AC225595.1
finished
37409 ABC14 5' / 5'
1 / 54437
- / 20680
33728
11.25
Identified
2014-07-23
agp2oracle
humpub
Certificate approved
14 CMB9-65A1
Hschr11_1_ctg3
cmb9E65A1
-
-
AP005140.4
finished
112601 CMB9        
  GAP (type-3) length unknown                  
16 RP11-494M8
Hschr11_1_ctg5
CONTAINER
bA494M8
EPN details
Externally Finished
21-JAN-13
AC044810.7
finished
194297 RPCI-11.2 3' / 3'
58104 / 42900
103926 / -
42900
33.54
Identified
2014-07-24
fetch_ncbi...
humpub
Certificate approved
17 ABC10-1605870K7
Hschr11_1_ctg5
CONTAINED
f10A1605870K7
-
-
AC209551.4
finished
42900 ABC10 5' / 5'
1 / 90372
- / 58104
42900
33.54
Identified
2014-07-24
fetch_ncbi...
humpub
Certificate approved
16 RP11-494M8
Hschr11_1_ctg5
CONTAINER
bA494M8
EPN details
Externally Finished
21-JAN-13
AC044810.7
finished
194297 RPCI-11.2        
  GAP (type-3) length unknown                  
19 RP13-25N22
Hschr11_1_ctg6
CONTAINER
bB25N22
EPN details
Externally Finished
21-JAN-13
AP006285.2
finished
190267 RPCI-13.1 3' / 5'
25510 / 1
133340 / -
37127
20.62
Identified
2014-07-24
fetch_ncbi...
humpub
Certificate approved
20 ABC10-44565900B4
Hschr11_1_ctg6
CONTAINED
f10A44565900B4
-
-
AC211344.3
finished
37127 ABC10 3' / 5'
37127 / 56928
- / 25510
37127
20.62
Identified
2014-07-24
fetch_ncbi...
humpub
Certificate approved
19 RP13-25N22
Hschr11_1_ctg6
CONTAINER
bB25N22
EPN details
Externally Finished
21-JAN-13
AP006285.2
finished
190267 RPCI-13.1        
  GAP (type-3) length unknown                  
22 RP11-19N21
Hschr11_1_ctg7
CONTAINER
bA19N21
-
-
AC013791.9
finished
174569 RPCI-11.1 5' / 3'
126563 / 378
126184 / -
378
0.26
Identified
2014-07-24
fetch_ncbi...
humpub
 
23
Hschr11_1_ctg7
CONTAINED
KF455305
-
-
KF455305.1
finished
378 - 5' / 3'
1 / 126184
- / 48007
378
0.26
Identified
2014-07-24
fetch_ncbi...
humpub
 
22 RP11-19N21
Hschr11_1_ctg7
CONTAINER
bA19N21
-
-
AC013791.9
finished
174569 RPCI-11.1 5' / 3'
122590 / 387
122202 / -
387
0.26
Identified
2014-07-24
fetch_ncbi...
humpub
 
24
Hschr11_1_ctg7
CONTAINED
KF455306
-
-
KF455306.1
finished
387 - 5' / 3'
1 / 122202
- / 51980
387
0.26
Identified
2014-07-24
fetch_ncbi...
humpub
 
22 RP11-19N21
Hschr11_1_ctg7
CONTAINER
bA19N21
-
-
AC013791.9
finished
174569 RPCI-11.1 5' / 5'
121929 / 1
1 / -
120249
2.37
Identified
2014-07-24
fetch_ncbi...
humpub
Certificate approved
25 HSAC001228
Hschr11_1_ctg7
HSAC001228
-
-
AC001228.1
finished
244254 -        
  GAP (type-3) length unknown                  
27 RP13-46H24
Hschr11_1_ctg8
bB46H24
EPN details
Externally Finished
21-JAN-13
AC137894.5
finished
165000 RPCI-13.1 3' / 5'
165000 / 59245
- / -
59236
0.09
Identified
2014-07-24
fetch_ncbi...
humpub
 
28 CTD-2647G13
Hschr11_1_ctg8
bK2647G13
-
-
AC138374.2
finished
196424 CIT-HSP-D2        

Statistics

Clone Summary

Number of gaps
8
Gap types
type-3
8
Total clones
20
Clone HTGS Phases
finished
20
Number of clones w/o accession
0

Overlap Summary

Total overlap length of fin clones
208,792
Total finished length of fin clones w/ overlap
2,189,682
Total finished length of fin clones w/o overlap
1,980,890
Total overlap length of fin+unfin clones
208,792
Total finished length of fin+unfin clones w/ overlap
2,189,682
Total finished length of fin+unfin clones w/o overlap
1,980,890

AGP errors

# rank accession seq_start seq_end strand error date
1 29 AC013791.9 126,563 122,202 1 For sequence AC013791.9 chr_length = -4360 which is less than 1! (start = 126563 end = 122202) This sequence may be redundant, or its overlaps are wrong Wed, 23 Jul 2014 23:10

Dovetails

# rank accession status length date
1 1 AC009638.9 unfinished 88,164 Wed, 23 Jul 2014 23:09
2 14 AP005140.4 unfinished 58,165 Wed, 23 Jul 2014 23:09
3 16 AC044810.7 unfinished 103,926 Wed, 23 Jul 2014 23:09
4 19 AP006285.2 unfinished 133,340 Wed, 23 Jul 2014 23:09
5 22 AC013791.9 unfinished 126,184 Wed, 23 Jul 2014 23:09

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Other links

* quick link - http://q.sanger.ac.uk/b54p87zw