\name{n240}
\alias{n240}
\docType{data}
\title{
NA19240 -- 3 million reads from chromosome 6 derived from 1000 genomes bam file
}
\description{
NA19240 -- 3 million reads from chromosome 6 derived from 1000 genomes bam file
}
\usage{data(n240)}
\format{
  The format is: \cr
List of 1 \cr
 $ :List of 13 \cr
  ..$ qname : chr [1:3000000] "EAS254_13:7:88:1639:15041" "EAS139_43:2:31:1128:9551" "EAS254_13:8:68:520:6861" "BGI-FC20AHFAAXX_6_26_477:352" ... \cr
  ..$ flag  : int [1:3000000] 35 35 35 16 35 35 35 0 35 35 ... \cr
  ..$ rname : Factor w/ 1 level "6": 1 1 1 1 1 1 1 1 1 1 ... \cr
  ..$ strand: Factor w/ 3 levels "-","+","*": 2 2 2 1 2 2 2 2 2 2 ... \cr
  ..$ pos   : int [1:3000000] 5001 5002 5004 5004 5005 5010 5012 5018 5018 5023 ... \cr
  ..$ qwidth: int [1:3000000] 51 51 51 36 51 51 36 36 36 45 ... \cr
  ..$ mapq  : int [1:3000000] 0 0 0 0 0 0 0 0 0 0 ... \cr
  ..$ cigar : chr [1:3000000] "51M" "51M" "51M" "36M" ... \cr
  ..$ mrnm  : Factor w/ 1 level "6": 1 1 1 NA 1 1 1 NA 1 1 ... \cr
  ..$ mpos  : int [1:3000000] 5163 5203 5170 NA 5156 5183 5199 NA 5252 5273 ... \cr
  ..$ isize : int [1:3000000] 214 253 218 NA 203 225 224 NA 271 296 ... \cr
  ..$ seq   :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots \cr
  .. .. ..@ super          :Formal class 'DNAString' [package "Biostrings"] with 6 slots \cr
  .. .. .. .. ..@ xdata          :Formal class 'RawPtr' [package "IRanges"] with 2 slots \cr
  .. .. .. .. .. .. ..@ xp                    :<externalptr>  \cr
  .. .. .. .. .. .. ..@ .link_to_cached_object:<environment: 0xc5354b8>  \cr
  .. .. .. .. ..@ offset         : int 0 \cr
  .. .. .. .. ..@ length         : int 118321039 \cr
  .. .. .. .. ..@ elementMetadata: NULL \cr
  .. .. .. .. ..@ elementType    : chr "ANYTHING" \cr
  .. .. .. .. ..@ metadata       : list() \cr
  .. .. ..@ ranges         :Formal class 'IRanges' [package "IRanges"] with 6 slots \cr
  .. .. .. .. ..@ start          : int [1:3000000] 1 52 103 154 190 241 292 328 364 400 ... \cr
  .. .. .. .. ..@ width          : int [1:3000000] 51 51 51 36 51 51 36 36 36 45 ... \cr
  .. .. .. .. ..@ NAMES          : NULL \cr
  .. .. .. .. ..@ elementMetadata: NULL \cr
  .. .. .. .. ..@ elementType    : chr "integer" \cr
  .. .. .. .. ..@ metadata       : list() \cr
  .. .. ..@ elementMetadata: NULL \cr
  .. .. ..@ elementType    : chr "ANYTHING" \cr
  .. .. ..@ metadata       : list() \cr
  ..$ qual  :Formal class 'PhredQuality' [package "Biostrings"] with 5 slots \cr
  .. .. ..@ super          :Formal class 'BString' [package "Biostrings"] with 6 slots \cr
  .. .. .. .. ..@ xdata          :Formal class 'RawPtr' [package "IRanges"] with 2 slots \cr
  .. .. .. .. .. .. ..@ xp                    :<externalptr>  \cr
  .. .. .. .. .. .. ..@ .link_to_cached_object:<environment: 0xc5354b8>  \cr
  .. .. .. .. ..@ offset         : int 0 \cr
  .. .. .. .. ..@ length         : int 118321039 \cr
  .. .. .. .. ..@ elementMetadata: NULL \cr
  .. .. .. .. ..@ elementType    : chr "ANYTHING" \cr
  .. .. .. .. ..@ metadata       : list() \cr
  .. .. ..@ ranges         :Formal class 'IRanges' [package "IRanges"] with 6 slots \cr
  .. .. .. .. ..@ start          : int [1:3000000] 1 52 103 154 190 241 292 328 364 400 ... \cr
  .. .. .. .. ..@ width          : int [1:3000000] 51 51 51 36 51 51 36 36 36 45 ... \cr
  .. .. .. .. ..@ NAMES          : NULL \cr
  .. .. .. .. ..@ elementMetadata: NULL \cr
  .. .. .. .. ..@ elementType    : chr "integer" \cr
  .. .. .. .. ..@ metadata       : list() \cr
  .. .. ..@ elementMetadata: NULL \cr
  .. .. ..@ elementType    : chr "ANYTHING" \cr
  .. .. ..@ metadata       : list() \cr
}
\details{
result of Rsamtools scanBam applied to a 3mm line excerpt from the SLX chr6 aligned reads for NA19240

update october 2010 to reflect modifications to cigar handling in Rsamtools
}
\source{
1000 genomes pilot data
}
%\references{
%%%  ~~ possibly secondary sources and usages ~~
%}
\examples{
data(n240)
sapply(n240[[1]], class)
}
\keyword{datasets}