Schema for Assembly - Assembly from Fragments
  Database: mm39    Primary Table: gold    Row Count: 22,273   Data last updated: 2020-07-27
Format description: How to get through chromosome based on fragments
fieldexampleSQL type info description
bin 608smallint(6) range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 3050000int(10) unsigned range start position in chromosome
chromEnd 3051641int(10) unsigned range end position in chromosome
ix 5int(11) range ix of this fragment (useless)
type Wchar(1) values (W)GS contig, (P)redraft, (D)raft, (F)inished or (O)ther
frag CAAA01096438.1varchar(255) values which fragment
fragStart 0int(10) unsigned range start position in frag
fragEnd 1641int(10) unsigned range end position in frag
strand +char(1) values + or - (orientation of fragment)

Sample Rows
 
binchromchromStartchromEndixtypefragfragStartfragEndstrand
608chr1305000030516415WCAAA01096438.101641+
608chr1305164130699916WLXEJ02000243.1121319563+
608chr1306999130721197WCAAA01188926.102128+
608chr1307211930733418WLXEJ02000243.12169322915+
608chr1307334130801429WCAAA01109096.106801+
9chr13080142330360610FAC157543.80223464-
76chr13303606345478711FAC157545.1246186197367+
76chr13454787366645812FAC157542.116211677+
76chr13666458385661413FAC102110.823576213732+
76chr13856614394844914FAC174931.2091835-

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

Assembly (gold) Track Description
 

Description

This track shows the sequences used in the Jun. 2020 mouse genome assembly.

Genome assembly procedures are covered in the NCBI assembly documentation.
NCBI also provides specific information about this assembly.

The definition of this assembly is from the AGP file delivered with the sequence. The NCBI document AGP Specification describes the format of the AGP file.

In dense mode, this track depicts the contigs that make up the currently viewed scaffold. Contig boundaries are distinguished by the use of alternating gold and brown coloration. Where gaps exist between contigs, spaces are shown between the gold and brown blocks. The relative order and orientation of the contigs within a scaffold is always known; therefore, a line is drawn in the graphical display to bridge the blocks.

Component types found in this track (with counts of that type in parentheses):

  • F - finished sequence (20,878)
  • W - whole genome shotgun (1,264)
  • O - other sequence (118)
  • P - pre draft (12)
  • A - active finishing (1)