ChromoView - clone / Assembly sequencing status

Human: Sub region GRC__HUMAN__ALT_REF_LOCI_1__18 (TPF updated: 2017-06-27)

TPF

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# Clone ext/Contig Clone int Acc/Fin
1 RP11-1030E3
Hschr18_1_ctg1_1
 bA1030E3
 AC105227.6
finished
2 RP11-2E13
Hschr18_1_ctg1_1
 bA2E13
 AC013759.6
finished
3 RP11-429H5
Hschr18_1_ctg1_1
 bA429H5
 AC090638.11
finished
  GAP (type-3) length unknown    
5 RP11-440L16
Hschr18_2_ctg1_1
CONTAINER		 bA440L16
 AC027216.6
finished
6 ABC9-43917900H23
Hschr18_2_ctg1_1
CONTAINED		 f9A43917900H23
 AC208322.3
finished
5 RP11-440L16
Hschr18_2_ctg1_1
CONTAINER		 bA440L16
 AC027216.6
finished
  GAP (type-3) length unknown    
8 RP11-117L4
Hschr18_1_ctg2
CONTAINER		 bA117L4
 AC103951.7
finished
9 ABC13-47619300L5
Hschr18_1_ctg2
CONTAINED		 f13A47619300L5
 AC216971.3
finished
8 RP11-117L4
Hschr18_1_ctg2
CONTAINER		 bA117L4
 AC103951.7
finished
  GAP (type-3) length unknown    
11 CTD-2541J13
Hschr18_2_ctg2
CONTAINER		 bK2541J13
 AC110597.7
finished
12 ABC7-42509700P1
Hschr18_2_ctg2
CONTAINED		 f7A42509700P1
 AC231988.2
finished
11 CTD-2541J13
Hschr18_2_ctg2
CONTAINER		 bK2541J13
 AC110597.7
finished
13 ABC8-718040A12
Hschr18_2_ctg2
CONTAINED		 f8A718040A12
 AC231982.2
finished
11 CTD-2541J13
Hschr18_2_ctg2
CONTAINER		 bK2541J13
 AC110597.7
finished
14 UNKNOWN
Hschr18_2_ctg2
 UNKNOWN
-
  GAP (type-3) length unknown    
16 RP11-123I22
Hschr18_1_ctg2_1
CONTAINER		 bA123I22
 AC012572.17
finished
17 ABC10-45522900G22
Hschr18_1_ctg2_1
CONTAINED		 f10A45522900G22
 AC213028.5
finished
16 RP11-123I22
Hschr18_1_ctg2_1
CONTAINER		 bA123I22
 AC012572.17
finished
  GAP (type-3) length unknown    
19 RP11-849I19
Hschr18_2_ctg2_1
CONTAINER		 bA849I19
 AC099689.4
finished
20 ABC9-46272800J3
Hschr18_2_ctg2_1
CONTAINED		 f9A46272800J3
 AC214178.3
finished
19 RP11-849I19
Hschr18_2_ctg2_1
CONTAINER		 bA849I19
 AC099689.4
finished
  GAP (type-3) length unknown    
22 RP11-567M16
Hschr18_3_ctg2_1
CONTAINER		 bA567M16
 AC068473.19
finished
23 ABC13-49696800L24
Hschr18_3_ctg2_1
CONTAINED		 f13A49696800L24
 AC215996.3
finished
22 RP11-567M16
Hschr18_3_ctg2_1
CONTAINER		 bA567M16
 AC068473.19
finished
24
Hschr18_3_ctg2_1
CONTAINED		 KF456464
 KF456464.1
finished
22 RP11-567M16
Hschr18_3_ctg2_1
CONTAINER		 bA567M16
 AC068473.19
finished
  GAP (type-3) length unknown    
26 RP11-115N12
Hschr18_4_ctg1_1
CONTAINER		 bA115N12
 AC018517.7
finished
27
Hschr18_4_ctg1_1
CONTAINED		 KF456390
 KF456390.1
finished
26 RP11-115N12
Hschr18_4_ctg1_1
CONTAINER		 bA115N12
 AC018517.7
finished
28 ABC9-45237700A3
Hschr18_4_ctg1_1
CONTAINED		 f9A45237700A3
 AC226767.2
finished
26 RP11-115N12
Hschr18_4_ctg1_1
CONTAINER		 bA115N12
 AC018517.7
finished
29
Hschr18_4_ctg1_1
CONTAINED		 KF456389
 KF456389.1
finished
26 RP11-115N12
Hschr18_4_ctg1_1
CONTAINER		 bA115N12
 AC018517.7
finished
  GAP (type-3) length unknown    
31 RP11-863N1
Hschr18_5_ctg1_1
CONTAINER		 bA863N1
 AC099849.4
finished
32 ABC12-47954900M11
Hschr18_5_ctg1_1
CONTAINED		 f12A47954900M11
 AC221035.4
finished
31 RP11-863N1
Hschr18_5_ctg1_1
CONTAINER		 bA863N1
 AC099849.4
finished

AGP

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AGP_S AGP_E Rank Status Acc.ver Clone_S Clone_E Str
1 84557 1 FClick to retrieve finished assembled sequence in green bar: rank(s) 1 - 3 AC105227.6 101012 185568 -
84558 251257 2 FClick to retrieve finished assembled sequence in green bar: rank(s) 1 - 3 AC013759.6 1 166700 -
251258 339964 3 FClick to retrieve finished assembled sequence in green bar: rank(s) 1 - 3 AC090638.11 91723 180429 +
339965 389964 4 N 50000 contig no
389965 499328 5 FClick to retrieve finished assembled sequence in green bar: rank(s) 5 - 7 AC027216.6 1 109364 +
499329 539848 6 FClick to retrieve finished assembled sequence in green bar: rank(s) 5 - 7 AC208322.3 1 40520 +
539849 566889 7 FClick to retrieve finished assembled sequence in green bar: rank(s) 5 - 7 AC027216.6 143803 170843 +
566890 616889 8 N 50000 contig no
616890 666229 9 FClick to retrieve finished assembled sequence in green bar: rank(s) 9 - 11 AC103951.7 1 49340 +
666230 706823 10 FClick to retrieve finished assembled sequence in green bar: rank(s) 9 - 11 AC216971.3 1 40594 -
706824 798581 11 FClick to retrieve finished assembled sequence in green bar: rank(s) 9 - 11 AC103951.7 77043 168800 +
798582 848581 12 N 50000 contig no
848582 909627 13 F AC110597.7
Orientation and overlap information are inconsistent for container clone AC110597 and contained clone AC231982 		1 61046 +
909628 909628 14 FClick to retrieve finished assembled sequence in green bar: rank(s) 14 - 14 AC231988.2 34660 34660 -
909629 1028893 15 F AC110597.7
Orientation and overlap information are inconsistent for container clone AC110597 and contained clone AC231982 		61046 180310 +
1028894 1078893 16 N 50000 clone no
1078894 1128893 17 N 50000 contig no
1128894 1251859 18 FClick to retrieve finished assembled sequence in green bar: rank(s) 18 - 20 AC012572.17 1 122966 +
1251860 1295288 19 FClick to retrieve finished assembled sequence in green bar: rank(s) 18 - 20 AC213028.5 1 43429 -
1295289 1310916 20 FClick to retrieve finished assembled sequence in green bar: rank(s) 18 - 20 AC012572.17 157010 172637 +
1310917 1360916 21 N 50000 contig no
1360917 1461080 22 FClick to retrieve finished assembled sequence in green bar: rank(s) 22 - 24 AC099689.4 1 100164 +
1461081 1498188 23 FClick to retrieve finished assembled sequence in green bar: rank(s) 22 - 24 AC214178.3 1 37108 +
1498189 1567870 24 FClick to retrieve finished assembled sequence in green bar: rank(s) 22 - 24 AC099689.4 131838 201519 +
1567871 1617870 25 N 50000 contig no
1617871 1667944 26 FClick to retrieve finished assembled sequence in green bar: rank(s) 26 - 30 AC068473.19 1 50074 +
1667945 1704777 27 FClick to retrieve finished assembled sequence in green bar: rank(s) 26 - 30 AC215996.3 1 36833 -
1704778 1707115 28 FClick to retrieve finished assembled sequence in green bar: rank(s) 26 - 30 AC068473.19 81154 83491 +
1707116 1707178 29 FClick to retrieve finished assembled sequence in green bar: rank(s) 26 - 30 KF456464.1 1 63 +
1707179 1799345 30 FClick to retrieve finished assembled sequence in green bar: rank(s) 26 - 30 AC068473.19 83555 175721 +
1799346 1849345 31 N 50000 contig no
1849346 1849463 32 FClick to retrieve finished assembled sequence in green bar: rank(s) 32 - 38 AC018517.7 1 118 +
1849464 1849813 33 FClick to retrieve finished assembled sequence in green bar: rank(s) 32 - 38 KF456390.1 1 350 -
1849814 1865221 34 FClick to retrieve finished assembled sequence in green bar: rank(s) 32 - 38 AC018517.7 469 15876 +
1865222 1901440 35 FClick to retrieve finished assembled sequence in green bar: rank(s) 32 - 38 AC226767.2 1 36219 -
1901441 1931028 36 FClick to retrieve finished assembled sequence in green bar: rank(s) 32 - 38 AC018517.7 46975 76562 +
1931029 1931116 37 FClick to retrieve finished assembled sequence in green bar: rank(s) 32 - 38 KF456389.1 1 88 -
1931117 2035383 38 FClick to retrieve finished assembled sequence in green bar: rank(s) 32 - 38 AC018517.7 76651 180917 +
2035384 2085383 39 N 50000 contig no
2085384 2217175 40 FClick to retrieve finished assembled sequence in green bar: rank(s) 40 - 42 AC099849.4 1 131792 +
2217176 2255490 41 FClick to retrieve finished assembled sequence in green bar: rank(s) 40 - 42 AC221035.4 1 38315 -
2255491 2291669 42 FClick to retrieve finished assembled sequence in green bar: rank(s) 40 - 42 AC099849.4 164428 200606 +

Details

Component Sanger::HumPub::ChromoView failed to execute

Statistics

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Clone Summary

Number of gaps
8
Gap types
type-3
8
Total clones
24
Clone HTGS Phases
finished
23
Number of clones w/o accession
1
Clones w/o htgs phase
1
Non-htgs clonenames
UNKNOWN (project unknown)

Overlap Summary

Total overlap length of fin clones
403,180
Total finished length of fin clones w/ overlap
2,324,314
Total finished length of fin clones w/o overlap
1,921,134
Total overlap length of fin+unfin clones
403,180
Total finished length of fin+unfin clones w/ overlap
2,324,314
Total finished length of fin+unfin clones w/o overlap
1,921,134

AGP errors

# rank accession seq_start seq_end strand error date
1 15 AC110597.7 61,046 180,310 1 Orientation and overlap information are inconsistent for container clone AC110597 and contained clone AC231982 Mon, 26 Jun 2017 23:24

Dovetails

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# rank accession status length date
1 5 AC027216 unfinished 27,041 Mon, 26 Jun 2017 23:24
2 8 AC103951 unfinished 91,758 Mon, 26 Jun 2017 23:24
3 11 AC110597 unfinished 98,566 Mon, 26 Jun 2017 23:24
4 16 AC012572 unfinished 122,966 Mon, 26 Jun 2017 23:24
5 19 AC099689 unfinished 69,682 Mon, 26 Jun 2017 23:24
6 22 AC068473 unfinished 94,568 Mon, 26 Jun 2017 23:24
7 26 AC018517 unfinished 180,449 Mon, 26 Jun 2017 23:24
8 31 AC099849 unfinished 36,179 Mon, 26 Jun 2017 23:24

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