Schema for Clone Ends - Mapping of clone libraries end placements
  Database: mm10    Primary Table: cloneEndRP24    Row Count: 50,849   Data last updated: 2016-03-02
Format description: Browser extensible data
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 9smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 3049731int(10) unsigned range Start position in chromosome
chromEnd 3214231int(10) unsigned range End position in chromosome
name RP24-86G11varchar(255) values Name of item
score 1000int(10) unsigned range Optional score, nominal range 0-1000
strand +char(1) values + or -
thickStart 3049731int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 3214231int(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 423,536longblob   Comma separated list of block sizes
chromStarts 0,163964longblob   Start positions relative to chromStart

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
9chr130497313214231RP24-86G111000+3049731321423102423,5360,163964
9chr130623733246494RP24-144B201000+3062373324649402488,8120,183309
9chr131194913273720RP24-388F151000+3119491327372002734,6180,153611
9chr131278223338361RP24-315L111000+3127822333836102650,6830,209856
610chr133171563320710RP24-129B181000+3317156332071002754,8390,2715
76chr133313283507871RP24-100L111000+3331328350787102484,1480,176395
76chr133592803551007RP24-271O221000+3359280355100702659,5960,191131
76chr133830663531871RP24-265O121000+3383066353187102481,3170,148488
76chr134000693552105RP24-186G201000+3400069355210502525,5940,151442
76chr134333143570956RP24-130L231000+3433314357095602416,6330,137009

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.