Clone Ends Track Settings

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Mapping of clone libraries end placements (All Mapping and Sequencing tracks)

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*Source*	Riken	Chori	Placements

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	Source^↓1	Track Name^↓2
hide	Riken	Riken Bioresource Center DNA Bank RNB1	schema
hide	Riken	Riken Bioresource Center DNA Bank RNB2	schema
hide	Chori	CHORI BACPAC Resources Center (BPRC) CHORI-230	schema
hide	Chori	CHORI BACPAC Resources Center (BPRC) RPCI-32	schema
hide	Placements	Clone end placements dropped at UCSC, map distance 3X median library size	schema
hide	Placements	Clone end placements overlap coverage on the forward strand	schema
hide	Placements	Clone end placements overlap coverage on the reverse strand	schema
hide	Placements	Clone end placements that map to multiple locations in the genome	schema

Description

This track shows the NCBI clone end mappings from the NCBI Clone DB database.

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/Rattus_norvegicus/ *.GCF_000001895.5.102.*.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.

Click through on displayed items to the Clone DB database information, including Clone DB distributor references.

clone information from NCBI Clone DB and UCSC mapping statistics
library name	total clones	total end sequences	NCBI mapped ends	UCSC filtered ends	UCSC dropped	per-cent dropped
RNB1	168,885	307,263	134,215	124,987	9,228	6.88
RNB2	115,060	331,272	96,829	89,108	7,721	7.97
CH230	192,416	227,486	83,816	78,516	5,300	6.32
RP32	2,883	294	106	105	1	0.94

Credits

Additional information about the clone, including how it can be obtained, may be found at the NCBI Clone Registry. To view the registry entry for a specific clone, open the details page for the clone and click on its name at the top of the page.