Schema for Clone Ends - Mapping of clone libraries end placements
  Database: mm10    Primary Table: cloneEndMHPP    Row Count: 28,550   Data last updated: 2016-03-02
Format description: Browser extensible data
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 608smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 3054487int(10) unsigned range Start position in chromosome
chromEnd 3062311int(10) unsigned range End position in chromosome
name MHPP-378N7varchar(255) values Name of item
score 1000int(10) unsigned range Optional score, nominal range 0-1000
strand -char(1) values + or -
thickStart 3054487int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 3062311int(10) unsigned range End of where display should be thick (stop codon)
reserved 0int(10) unsigned range Used as itemRgb as of 2004-11-22
blockCount 2int(10) unsigned range Number of blocks
blockSizes 687,446longblob   Comma separated list of block sizes
chromStarts 0,7378longblob   Start positions relative to chromStart

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
608chr130544873062311MHPP-378N71000-3054487306231102687,4460,7378
608chr130544873062311MHPP-378N81000-3054487306231102667,5500,7274
611chr134589003468411MHPP-280J241000+3458900346841102657,5470,8964
611chr135153963524072MHPP-395B241000-3515396352407202580,7050,7971
611chr135153963524072MHPP-97F191000-3515396352407202573,5790,8097
76chr135332543542293MHPP-273D101000-3533254354229302734,7560,8283
76chr135332543542293MHPP-72I51000-3533254354229302646,7790,8260
76chr137988303806731MHPP-182P151000-3798830380673102650,7590,7142
614chr138538283862946MHPP-391F141000-3853828386294602872,6880,8430
615chr139420263948909MHPP-19E11000+3942026394890902859,8160,6067

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Clone Ends (cloneEndSuper) Track Description
 

Description

This track shows the NCBI clone end predictions from the retired NCBI Clone DB database. Libraries with more than 20,000 clones are included in this track display.

Bacterial artificial chromosomes (BACs) are a key part of many large-scale sequencing projects. A BAC typically consists of 50 - 300 kb of DNA. During the early phase of a sequencing project, it is common to sequence a single read (approximately 500 bases) off each end of a large number of BACs. Later on in the project, these BAC end reads can be mapped to the genome sequence.

These BAC end pairs can be useful for validating the assembly over relatively long ranges. In some cases, the BACs are useful biological reagents. This track can also be used for determining which BAC contains a given gene, useful information for certain wet lab experiments.

The scoring scheme used for this annotation assigns 1000 to an alignment when the BAC end pair aligns to only one location in the genome (after filtering). When a BAC end pair or clone aligns to multiple locations, the score is calculated as 1500/(number of alignments).

Display Conventions and Configuration

Items in this track are colored according to their strand orientation. Blue indicates alignment to the forward strand, and green indicates alignment to the negative strand.

Methods

The mappings of these BAC end sequences are taken directly from the NCBI Clone DB FTP site ftp.ncbi.nih.gov/repository/clone/reports/Mus_musculus/ *.GCF_000001635.22.103.*.gff files.

UCSC filtered the NCBI Clone DB mapped ends to drop ends that mapped to a region that was three times longer than the median size of the clones in the library. Only libraries with more than 20,000 clones are included in this track display.

library
name		 total
clones		 total end
sequences		 NCBI mapped
ends		 UCSC filtered
ends		 UCSC
dropped		 percent
dropped
B6Ng01128,007253,63898,47895,8372,6412.68
bMQ129,826244,22275,67172,5403,1314.14
C3H86,696169,66543,69042,3781,3123.00
CH2993,023340,27252,32050,6211,6993.25
DN180,218665,070106,463100,4725,9915.63
MHPN118,658208,70761,94258,5823,3605.42
MHPP67,769112,08130,59428,5502,0446.68
MSMg01175,178337,47183,67778,7724,9055.86
RP23175,999553,27485,08283,0622,0202.37
RP24163,859294,21752,47050,8491,6213.09
WI1907,2131,822,723337,591324,25913,3323.95

Credits

Additional information about the clone, including how it can be obtained, was available at the retired NCBI Clone Registry. NCBI will continue to produce and make genomic clone placements available as annotations in NCBI's Genome Data Viewer (GDV) using the sequence data currently in Clone DB. Clone DB users should refer to MGI for their continuing research needs.

Please contact NCBI with any comments, concerns, or if you need help with the use of Clone DB data.