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 |
|---|
| B6Ng01 | 128,007 | 253,638 | 98,478 | 95,837 | 2,641 | 2.68 |
|---|
| bMQ | 129,826 | 244,222 | 75,671 | 72,540 | 3,131 | 4.14 |
|---|
| C3H | 86,696 | 169,665 | 43,690 | 42,378 | 1,312 | 3.00 |
|---|
| CH29 | 93,023 | 340,272 | 52,320 | 50,621 | 1,699 | 3.25 |
|---|
| DN | 180,218 | 665,070 | 106,463 | 100,472 | 5,991 | 5.63 |
|---|
| MHPN | 118,658 | 208,707 | 61,942 | 58,582 | 3,360 | 5.42 |
|---|
| MHPP | 67,769 | 112,081 | 30,594 | 28,550 | 2,044 | 6.68 |
|---|
| MSMg01 | 175,178 | 337,471 | 83,677 | 78,772 | 4,905 | 5.86 |
|---|
| RP23 | 175,999 | 553,274 | 85,082 | 83,062 | 2,020 | 2.37 |
|---|
| RP24 | 163,859 | 294,217 | 52,470 | 50,849 | 1,621 | 3.09 |
|---|
| WI1 | 907,213 | 1,822,723 | 337,591 | 324,259 | 13,332 | 3.95 |
|---|
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.
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