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table bigPsl
"bigPsl pairwise alignment"
(
string chrom; "Reference sequence chromosome or scaffold"
uint chromStart; "Start position in chromosome"
uint chromEnd; "End position in chromosome"
string name; "Name or ID of item, ideally both human readable and unique"
uint score; "Score (0-1000)"
char[1] strand; "+ or - indicates whether the query aligns to the + or - strand on the reference"
uint thickStart; "Start of where display should be thick (start codon)"
uint thickEnd; "End of where display should be thick (stop codon)"
uint reserved; "RGB value (use R,G,B string in input file)"
int blockCount; "Number of blocks"
int[blockCount] blockSizes; "Comma separated list of block sizes"
int[blockCount] chromStarts; "Start positions relative to chromStart"
uint oChromStart; "Start position in other chromosome"
uint oChromEnd; "End position in other chromosome"
char[1] oStrand; "+ or -, - means that psl was reversed into BED-compatible coordinates"
uint oChromSize; "Size of other chromosome."
int[blockCount] oChromStarts; "Start positions relative to oChromStart or from oChromStart+oChromSize depending on strand"
lstring oSequence; "Sequence on other chrom (or edit list, or empty)"
string oCDS; "CDS in NCBI format"
uint chromSize; "Size of target chromosome"
uint match; "Number of bases matched."
uint misMatch; "Number of bases that don't match"
uint repMatch; "Number of bases that match but are part of repeats"
uint nCount; "Number of 'N' bases"
uint seqType; "0=empty, 1=nucleotide, 2=amino_acid"
)
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