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  • agali
    Junior Member
    • Jul 2010
    • 4

    #1

    Corona Lite - output statistic file for matching reads

    Hello everyone!

    I am just starting my adventure with SOLiD sequencing. I am using Corona Lite 4.2.1 for the mapping to reference genome. In the output statistic files for mapped reads I am getting:

    "28591842 total beads found 75811 Mapped Reads using parameter settings listed below. Mapped Reads at Read Length 35 0 mismatches 46617 ( 61.49%)
    1 mismatches 14704 ( 19.40%) 61321 ( 80.89%) 2 mismatches 14490 ( 19.11%) 75811 (100.00%)

    Uniquely Placed Beads 0 mismatches 44808 ( 0.16%)
    1 mismatches 13183 ( 0.05%) 57991 ( 0.20%) 2 mismatches 12693 ( 0.04%) 70684 ( 0.25%)

    Valid Adjacents within Uniquely Placed Beads 0 valid adjacents 53677 ( 0.19%)
    1 valid adjacents 6648 ( 0.02%) 60325 ( 0.21%)

    Errors within Uniquely Placed Tags Total Errors 38533 Single Errors 24457 (63.47% of Total) Adjacent Errors 7038 (36.53% of total) Valid 6648 (34.51% of Total) (94.46% of Adjacent Errors) Invalid 390 (2.02% of Total) (5.54% of Adjacent Errors)"

    Could anybody please tell how to interpret the percentage of uniquely placed beads and where the Total number of errors came from?

    Thank you!

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