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6
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1 table bigPsl
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2 "bigPsl pairwise alignment"
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3 (
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4 string chrom; "Reference sequence chromosome or scaffold"
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5 uint chromStart; "Start position in chromosome"
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6 uint chromEnd; "End position in chromosome"
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7 string name; "Name or ID of item, ideally both human readable and unique"
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8 uint score; "Score (0-1000)"
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9 char[1] strand; "+ or - for strand"
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10 uint thickStart; "Start of where display should be thick (start codon)"
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11 uint thickEnd; "End of where display should be thick (stop codon)"
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12 uint reserved; "RGB value (use R,G,B string in input file)"
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13 int blockCount; "Number of blocks"
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14 int[blockCount] blockSizes; "Comma separated list of block sizes"
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15 int[blockCount] chromStarts; "Start positions relative to chromStart"
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16
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17 uint oChromStart;"Start position in other chromosome"
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18 uint oChromEnd; "End position in other chromosome"
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19 char[1] oStrand; "+ or - for other strand"
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20 uint oChromSize; "Size of other chromosome."
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21 int[blockCount] oChromStarts; "Start positions relative to oChromStart"
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22
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23 lstring oSequence; "Sequence on other chrom (or edit list, or empty)"
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24 string oCDS; "CDS in NCBI format"
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25
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26 uint chromSize;"Size of target chromosome"
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27
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28 uint match; "Number of bases matched."
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29 uint misMatch; " Number of bases that don't match "
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30 uint repMatch; " Number of bases that match but are part of repeats "
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31 uint nCount; " Number of 'N' bases "
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32 )
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33
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