Schema for Alignment - Alternate mouse strains, alignments to reference genome
  Database: mm10    Primary Table: altSeqLiftOverPslStrains1    Row Count: 578   Data last updated: 2012-11-09
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 16smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 538100int(10) unsigned range Number of bases that match that aren't repeats
misMatches 1973int(10) unsigned range Number of bases that don't match
repMatches 272898int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 0int(10) unsigned range Number of inserts in target
tBaseInsert 0int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName chr1_JH584320_1varchar(255) values Query sequence name
qSize 1003859int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 1003859int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 195471971int(10) unsigned range Target sequence size
tStart 60640808int(10) unsigned range Alignment start position in target
tEnd 63588262int(10) unsigned range Alignment end position in target
blockCount 597int(10) unsigned range Number of blocks in alignment
blockSizes 493,851,652,3713,173,159,49...longblob   Size of each block
qStarts 0,493,1344,1997,5710,5883,6...longblob   Start of each block in query.
tStarts 60640808,60641315,60642169,...longblob   Start of each block in target.

Connected Tables and Joining Fields
        mm10.chromInfo.chrom (via altSeqLiftOverPslStrains1.tName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
16538100197327289800000+chr1_JH584320_1100385901003859chr11954719716064080863588262597493,851,652,3713,173,159,4990,2474,4969,613,1477,155,1301,1365,3,760,3765,49,197,222,574,710,1083,2543,1290,1432,1107,3870,626,7 ...0,493,1344,1997,5710,5883,6042,11032,13507,18476,19089,20572,20729,22030,23396,23414,24175,27940,27989,28216,28439,29014,29724,3 ...60640808,60641315,60642169,60642821,60646549,60646724,60646887,60651878,60654352,60659322,60659939,60661416,60661571,60662878,60 ...
0212641039524123370700000+chr1_JH584321_1376095703760957chr119547197165597864692652546558198,1516,360,6,368,60,700,829,1421,431,44,98,225,27,134,34,178,328,117,518,54,224,275,461,601,69,676,44,49,81,195,110,530,3,215, ...0,201,1717,2080,2091,2459,2521,3221,4053,5475,5906,5954,6052,6287,6317,6451,6485,6665,6993,7114,7633,7687,15770,16045,16517,1711 ...65597864,65598062,65599580,65599940,65599946,65600315,65600375,65601078,65601907,65603328,65603762,65603806,65603906,65604131,65 ...
108624959300000+chr1_JH584321_13760957203245203592chr119547197165771258657716112271,76,203245,203516,65771258,65771535,
10872731216500000-chr1_JH584321_13760957323705324156chr11954719716588586465886314250,400,3436801,3436852,65885864,65885914,
109082724000000+chr1_JH584321_13760957699332700194chr119547197166288276662891436347,230,12,160,17,85,699332,699679,699911,699923,700083,700109,66288276,66288632,66288862,66288875,66289041,66289058,
1093621000000+chr1_JH584321_1376095711231551123220chr11954719716671558066715643331,5,27,1123155,1123187,1123193,66715580,66715611,66715616,
10941643000000+chr1_JH584321_1376095712473571247524chr119547197166843792668439591167,1247357,66843792,
109440515000000+chr1_JH584321_1376095712471041247524chr119547197166843959668443791420,1247104,66843959,
1094394000000+chr1_JH584321_1376095712473981247441chr11954719716684437966844422143,1247398,66844379,
109440316000000+chr1_JH584321_1376095712471051247524chr119547197166844422668448411419,1247105,66844422,

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

Alignment (altSeqLiftOverPslStrains1) Track Description
 

Description

This track shows alternate mouse strain sequences indicated by the GRC (Genome Reference Consortium) mapped to the GRCm38 (mm10) reference sequence in an effort to provide the best possible reference assembly for the mouse genome. The GRC does this by generating multiple representations, alternate loci, for regions that are too complex to be represented by a single path. This allows users who are interested in a specific locus to get an improved representation without affecting users who need chromosome coordinate stability.

Alignment

The Alignment track is the PSL representation of the lastz chained alignments of the alternate strain sequences to their mapped location on the reference sequence. This PSL representation allows the side-by-side alignment to be viewed. It was created from the lastz chained alignments using the chainToPsl kent source utility. This track follows the display conventions for PSL alignment tracks. Alignments are displayed in black and, depending on the track configuration settings, may be interspersed with vertical orange lines.

Alternate strains

Items in the Alt. strains track indicate where the alternate mouse strain sequences map to the reference genome location. Clicking on an item in this track will display the detail page for that item, including a link to the nucleotide sequence at NCBI/GenBank for the alternate mouse strain. Data points in this track are always displayed in red.

The locations of the Alternate strains were established by NCBI and specified in the alt_scaffold_placement.txt files at, for example, strain NOD_ShiLtJ:
GRCm38.p1/NOD_ShiLtJ/alt_scaffolds/alt_scaffold_placement.txt. Note that each alternate strain has a unique directory at Mus_musculus/GRCm38.p1/.

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.

The axtChain program was developed at the University of California 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

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

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.

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.