Hello, The statistics come from the program Repeat Masker. They are intended for provide information about the quality of the match. This match is very strong.
From the details page (where the information you pasted in came from) and scroll down to the Methods. Links to the Repeat Masker web site are there that will include definitions for all of the statistics reported. Clicking through to the primary table (using the link View table schema) for the track lists brief descriptions for data attributes, but is not a substitute for reading the actual program documentation. Note the field "milliDel" - this is the data reported as "Deletions" in the UCSC browser interface. > Database: canFam2 Primary Table: rmsk (chr1_rmsk) Row Count: 226,564 > Format description: RepeatMasker .out record > field example SQL type info description > bin 607 smallint(5) unsigned range Indexing field to speed > chromosome range queries. > swScore 1357 int(10) unsigned range Smith Waterman > alignment score > milliDiv 298 int(10) unsigned range Base mismatches in > parts per thousand > milliDel 24 int(10) unsigned range Bases deleted in parts > per thousand > milliIns 7 int(10) unsigned range Bases inserted in parts > per thousand > genoName chr1 varchar(255) values Genomic sequence name > genoStart 3000005 int(10) unsigned range Start in genomic > sequence > genoEnd 3001054 int(10) unsigned range End in genomic sequence > genoLeft -122615202 int(11) range -#bases after match in genomic > sequence > strand - char(1) values Relative orientation + or - > repName CarSat1 varchar(255) values Name of repeat > repClass Satellite varchar(255) values Class of repeat > repFamily Satellite varchar(255) values Family of repeat > repStart -7 int(11) range Start (if strand is +) or -#bases after > match (if strand is -) in repeat sequence > repEnd 1067 int(11) range End in repeat sequence > repLeft 1 int(11) range -#bases after match (if strand is +) or > start (if strand is -) in repeat sequence > id 1 char(1) values First digit of id field in RepeatMasker .out > file. Best ignored. --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 2/18/10 5:41 AM, nerea bartolome wrote: > > > Dear Mr. /Mrs., > > I have a doubt about the Repeat Masker Information displayed for a SINE > element in the UCSC website. > > When looking into an specific gene of the Dog genome a get the information > pasted below for an specific SINE element in that gene. What does "Deletions > 1.1%" mean? > > > > > > > > > > > > > > RepeatMasker Information > Name: SINEC_Cf > Family: Lys > Class: SINE > SW Score: 1642 > Divergence: 2.1% > Deletions: 1.1% > Insertions: 0.0% > Begin in repeat: 1 > End in repeat: 189 > Left in repeat: 0 > Position: chr4:25902793-25902979 > Genomic Size: 187 > Strand: + > View DNA for this feature > View table schema > > Go to RepeatMasker track controls > > Data last updated: 2005-07-10 > > Thanking you in advance, > > NB > > > _________________________________________________________________ > ¿Aún no sabes qué móvil eres? ¡Descúbrelo aquí! > http://www.quemovileres.com/ > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
