ChromoView - clone / Assembly sequencing status

Human: Sub region GRC__HUMAN__ALT_REF_LOCI_1__18 (TPF updated: 2018-01-16)

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
Hschr18_2_ctg2
CONTAINED		 ABBA01056267
 ABBA01056267.1
finished
11 CTD-2541J13
Hschr18_2_ctg2
CONTAINER		 bK2541J13
 AC110597.7
finished
14 ABC8-718040A12
Hschr18_2_ctg2
CONTAINED		 f8A718040A12
 AC231982.2
finished
11 CTD-2541J13
Hschr18_2_ctg2
CONTAINER		 bK2541J13
 AC110597.7
finished
  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
  GAP (type-3) length unknown    
34 CTD-2015H3
HSCHR18_1_CTG1
 bK2015H3
 AP005057.2
finished
35 ABC10-43645600F20
HSCHR18_1_CTG1
 f10A43645600F20
 AC208950.3
finished
36 RP11-161I6
HSCHR18_1_CTG1
 bA161I6
 AP005481.2
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
Cannot find overlap between container clone AC110597 and contained clone ABBA01056267 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
Cannot find overlap between container clone AC110597 and contained clone ABBA01056267 and contained clone AC231982 		61046 180310 +
1028894 1078893 16 N 50000 contig no
1078894 1201859 17 FClick to retrieve finished assembled sequence in green bar: rank(s) 17 - 19 AC012572.17 1 122966 +
1201860 1245288 18 FClick to retrieve finished assembled sequence in green bar: rank(s) 17 - 19 AC213028.5 1 43429 -
1245289 1260916 19 FClick to retrieve finished assembled sequence in green bar: rank(s) 17 - 19 AC012572.17 157010 172637 +
1260917 1310916 20 N 50000 contig no
1310917 1411080 21 FClick to retrieve finished assembled sequence in green bar: rank(s) 21 - 23 AC099689.4 1 100164 +
1411081 1448188 22 FClick to retrieve finished assembled sequence in green bar: rank(s) 21 - 23 AC214178.3 1 37108 +
1448189 1517870 23 FClick to retrieve finished assembled sequence in green bar: rank(s) 21 - 23 AC099689.4 131838 201519 +
1517871 1567870 24 N 50000 contig no
1567871 1617944 25 FClick to retrieve finished assembled sequence in green bar: rank(s) 25 - 29 AC068473.19 1 50074 +
1617945 1654777 26 FClick to retrieve finished assembled sequence in green bar: rank(s) 25 - 29 AC215996.3 1 36833 -
1654778 1657115 27 FClick to retrieve finished assembled sequence in green bar: rank(s) 25 - 29 AC068473.19 81154 83491 +
1657116 1657178 28 FClick to retrieve finished assembled sequence in green bar: rank(s) 25 - 29 KF456464.1 1 63 +
1657179 1749345 29 FClick to retrieve finished assembled sequence in green bar: rank(s) 25 - 29 AC068473.19 83555 175721 +
1749346 1799345 30 N 50000 contig no
1799346 1799463 31 FClick to retrieve finished assembled sequence in green bar: rank(s) 31 - 37 AC018517.7 1 118 +
1799464 1799813 32 FClick to retrieve finished assembled sequence in green bar: rank(s) 31 - 37 KF456390.1 1 350 -
1799814 1815221 33 FClick to retrieve finished assembled sequence in green bar: rank(s) 31 - 37 AC018517.7 469 15876 +
1815222 1851440 34 FClick to retrieve finished assembled sequence in green bar: rank(s) 31 - 37 AC226767.2 1 36219 -
1851441 1881028 35 FClick to retrieve finished assembled sequence in green bar: rank(s) 31 - 37 AC018517.7 46975 76562 +
1881029 1881116 36 FClick to retrieve finished assembled sequence in green bar: rank(s) 31 - 37 KF456389.1 1 88 -
1881117 1985383 37 FClick to retrieve finished assembled sequence in green bar: rank(s) 31 - 37 AC018517.7 76651 180917 +
1985384 2035383 38 N 50000 contig no
2035384 2167175 39 FClick to retrieve finished assembled sequence in green bar: rank(s) 39 - 41 AC099849.4 1 131792 +
2167176 2205490 40 FClick to retrieve finished assembled sequence in green bar: rank(s) 39 - 41 AC221035.4 1 38315 -
2205491 2241669 41 FClick to retrieve finished assembled sequence in green bar: rank(s) 39 - 41 AC099849.4 164428 200606 +
2241670 2291669 42 N 50000 contig no
2291670 2373881 43 FClick to retrieve finished assembled sequence in green bar: rank(s) 43 - 45 AP005057.2 1 82212 +
2373882 2416334 44 FClick to retrieve finished assembled sequence in green bar: rank(s) 43 - 45 AC208950.3 1 42453 -
2416335 2459146 45 FClick to retrieve finished assembled sequence in green bar: rank(s) 43 - 45 AP005481.2 13189 56000 +

Details

Component Sanger::HumPub::ChromoView failed to execute

Statistics

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Clone Summary

Number of gaps
9
Gap types
type-3
9
Total clones
27
Clone HTGS Phases
finished
27
Number of clones w/o accession
0

Overlap Summary

Total overlap length of fin clones
426,150
Total finished length of fin clones w/ overlap
3,008,024
Total finished length of fin clones w/o overlap
2,581,874
Total overlap length of fin+unfin clones
426,150
Total finished length of fin+unfin clones w/ overlap
3,008,024
Total finished length of fin+unfin clones w/o overlap
2,581,874

AGP errors

# rank accession seq_start seq_end strand error date
1 15 AC110597.7 61,046 180,310 1 Cannot find overlap between container clone AC110597 and contained clone ABBA01056267 and contained clone AC231982 Mon, 15 Jan 2018 23:26

Dovetails

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# rank accession status length date
1 5 AC027216 unfinished 27,041 Mon, 15 Jan 2018 23:26
2 8 AC103951 unfinished 91,758 Mon, 15 Jan 2018 23:26
3 11 AC110597 unfinished 98,566 Mon, 15 Jan 2018 23:26
4 16 AC012572 unfinished 122,966 Mon, 15 Jan 2018 23:26
5 19 AC099689 unfinished 69,682 Mon, 15 Jan 2018 23:26
6 22 AC068473 unfinished 94,568 Mon, 15 Jan 2018 23:26
7 26 AC018517 unfinished 180,449 Mon, 15 Jan 2018 23:26
8 31 AC099849 unfinished 36,179 Mon, 15 Jan 2018 23:26

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