Schema for hg19 Chain/Net - Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments
  Database: rheMac3    Primary Table: netHg19    Row Count: 1,295,427   Data last updated: 2012-03-16
Format description: Database representation of a net of alignments.
fieldexampleSQL type description
bin 9smallint(5) unsigned Indexing field to speed chromosome range queries.
level 1int(10) unsigned Level of alignment
tName chr1varchar(255) Target chromosome
tStart 7int(10) unsigned Start on target
tEnd 3965806int(10) unsigned End on target
strand -char(1) Orientation of query. + or -
qName chr4varchar(255) Query chromosome
qStart 46553int(10) unsigned Start on query
qEnd 3817744int(10) unsigned End on query
chainId 48int(10) unsigned Associated chain Id with alignment details
ali 2819799int(10) unsigned Bases in gap-free alignments
score 181441082double Score - a number proportional to 100x matching bases
qOver -1int(11) Overlap with parent gap on query side. -1 for undefined
qFar -1int(11) Distance from parent gap on query side. -1 for undefined
qDup 52672int(11) Bases with two or more copies in query. -1 for undefined
type topvarchar(255) Syntenic type: gap/top/syn/nonsyn/inv
tN 442850int(11) Unsequenced bases on target. -1 for undefined
qN 55500int(11) Unsequenced bases on query. -1 for undefined
tR 1607797int(11) RepeatMasker bases on target. -1 for undefined
qR 1697691int(11) RepeatMasker bases on query. -1 for undefined
tNewR -1int(11) Lineage specific repeats on target. -1 for undefined
qNewR -1int(11) Lineage specific repeats on query. -1 for undefined
tOldR -1int(11) Bases of ancient repeats on target. -1 for undefined
qOldR -1int(11) Bases of ancient repeats on query. -1 for undefined
tTrf 211020int(11) Bases of tandem repeats on target. -1 for undefined
qTrf 244940int(11) Bases of tandem repeats on query. -1 for undefined

Connected Tables and Joining Fields
        rheMac3.chainHg19.id (via netHg19.chainId)
      rheMac3.chainHg19Link.chainId (via netHg19.chainId)

Sample Rows
 
binleveltNametStarttEndstrandqNameqStartqEndchainIdaliscoreqOverqFarqDuptypetNqNtRqRtNewRqNewRtOldRqOldRtTrfqTrf
91chr173965806-chr4465533817744482819799181441082-1-152672top4428505550016077971697691-1-1-1-1211020244940
5852chr1155313-chr438172263817595000-1-1-1gap00106318-1-1-1-1158369
5852chr1530543-chr438170023817002000-1-1-1gap00130-1-1-1-1130
5852chr1731750-chr438168253816825000-1-1-1gap00190-1-1-1-1190
5852chr19761005-chr438165603816589000-1-1-1gap00290-1-1-1-12929
5852chr121342148-chr438154053815405000-1-1-1gap0000-1-1-1-100
5852chr128262837-chr438147193814719000-1-1-1gap00110-1-1-1-100
5852chr143324348-chr438132003813223000-1-1-1gap0000-1-1-1-1140
5852chr155436051-chr438114613811976000-1-1-1gap00484466-1-1-1-11820
5852chr1865518811-chr438088153808860000-1-1-1gap77360114428-1-1-1-145845

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

hg19 Chain/Net (chainNetHg19) Track Description
 

Description

This track shows regions of the genome that are alignable to other genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown like introns.

Chain Track

The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to the rhesus genome using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both human and rhesus simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species.

The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the human assembly or an insertion in the rhesus assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of the rhesus genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes.

In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment.

Net Track

The net track shows the best human/rhesus chain for every part of the rhesus genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. The human sequence used in this annotation is from the Feb. 2009 (GRCh37/hg19) assembly.

Display Conventions and Configuration

Chain Track

By default, the chains to chromosome-based assemblies are colored based on which chromosome they map to in the aligning organism. To turn off the coloring, check the "off" button next to: Color track based on chromosome.

To display only the chains of one chromosome in the aligning organism, enter the name of that chromosome (e.g. chr4) in box next to: Filter by chromosome.

Net Track

In full display mode, the top-level (level 1) chains are the largest, highest-scoring chains that span this region. In many cases gaps exist in the top-level chain. When possible, these are filled in by other chains that are displayed at level 2. The gaps in level 2 chains may be filled by level 3 chains and so forth.

In the graphical display, the boxes represent ungapped alignments; the lines represent gaps. Click on a box to view detailed information about the chain as a whole; click on a line to display information about the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement.

Individual items in the display are categorized as one of four types (other than gap):

  • Top - the best, longest match. Displayed on level 1.
  • Syn - line-ups on the same chromosome as the gap in the level above it.
  • Inv - a line-up on the same chromosome as the gap above it, but in the opposite orientation.
  • NonSyn - a match to a chromosome different from the gap in the level above.

Methods

Chain track

Transposons that have been inserted since the human/rhesus split were removed from the assemblies. The abbreviated genomes were aligned with lastz, and the transposons were added back in. The resulting alignments were converted into axt format using the lavToAxt program. The axt alignments were fed into axtChain, which organizes all alignments between a single human chromosome and a single rhesus chromosome into a group and creates a kd-tree out of the gapless subsections (blocks) of the alignments. A dynamic program was then run over the kd-trees to find the maximally scoring chains of these blocks. The following matrix was used:

 ACGT
A90-330-236-356
C-330100-318-236
G-236-318100-330
T-356-236-33090

Chains scoring below a minimum score of "5000" were discarded; the remaining chains are displayed in this track. The linear gap matrix used with axtChain:
-linearGap=medium

tableSize    11
smallSize   111
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300

Net track

Chains were derived from lastz alignments, using the methods described on the chain tracks description pages, and sorted with the highest-scoring chains in the genome ranked first. The program chainNet was then used to place the chains one at a time, trimming them as necessary to fit into sections not already covered by a higher-scoring chain. During this process, a natural hierarchy emerged in which a chain that filled a gap in a higher-scoring chain was placed underneath that chain. The program netSyntenic was used to fill in information about the relationship between higher- and lower-level chains, such as whether a lower-level chain was syntenic or inverted relative to the higher-level chain. The program netClass was then used to fill in how much of the gaps and chains contained Ns (sequencing gaps) in one or both species and how much was filled with transposons inserted before and after the two organisms diverged.

Credits

Lastz (previously known as blastz) was developed at Pennsylvania State University by Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from Ross Hardison.

Lineage-specific repeats were identified by Arian Smit and his RepeatMasker program.

The axtChain program was developed at the University of California at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.

The browser display and database storage of the chains and nets were created by Robert Baertsch and Jim Kent.

The chainNet, netSyntenic, and netClass programs were developed at the University of California Santa Cruz by Jim Kent.

References

Harris, R.S. (2007) Improved pairwise alignment of genomic DNA Ph.D. Thesis, The Pennsylvania State University

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961