This work was supported by the National Science Foundation under Grant No. 0822258-DFBI

 Name                           Last modified      Size  Description
 Parent Directory                                    -   
 Gcanescens_BES.clipped.gff.bz2 2012-08-08 15:23  848K  Gcanescens_BES.clipped aligned to G. max
 Gcanescens_BES.fasta.bz2       2011-04-18 11:30   38M  Glycine canescens BAC-end sequence
 Gcanescens_BES.qual.bz2        2011-04-18 11:31   48M  quality scores for Gcanescens_BES.fasta
 Gcanescens_BES.clipped.bz2     2011-04-18 11:29   30M  quality-trimmed Gcanescens_BES.fasta

Glycine canescens BAC-end sequence from the SoyMap II project
=============================================================

CONTENTS
========

    Gcanescens_BES.clipped.bz2     - quality-trimmed Gcanescens_BES.fasta
    Gcanescens_BES.clipped.gff.bz2 - Gcanescens_BES.clipped aligned to G. max
    Gcanescens_BES.fasta.bz2       - Glycine canescens BAC-end sequence
    Gcanescens_BES.qual.bz2        - quality scores for Gcanescens_BES.fasta
    README.txt                     - This README file

BAC LIBRARY INFORMATION
=======================

    SOJ
    AGI constructed library
    GC_Bc
    HindIII cut
    146kb average insert size
    12x genome coverage
    Complete set 224 plates
    Sequencing 170

    13247.fasta.screen.qual
    =======================
    Phred20 Reads %ofReads
      0- 49  3025  2.3%     |X
     50- 99  1116  0.9%     |
    100-149   744  0.6%     |
    150-199   673  0.5%     |
    200-249   650  0.5%     |
    250-299   571  0.4%     |
    300-349   574  0.4%     |
    350-399   680  0.5%     |
    400-449   835  0.6%     |
    450-499  1087  0.8%     |
    500-549  1481  1.1%     |X
    550-599  2191  1.7%     |X
    600-649  3833  2.9%     |X
    650-699  7631  5.8%     |XXX
    700-749 14886 11.4%     |XXXXXX
    750-799 26528 20.3%     |XXXXXXXXXX
    800-849 35911 27.5%     |XXXXXXXXXXXXXX
    850-899 24894 19.1%     |XXXXXXXXXX
    900-949  3234  2.5%     |X
    950-999    16  0.0%     |

    Number of reads: 130,560
    Total bases: 132,409,333
    Total Phred 20 bases: 97,228,362
    Average length: 1014.2
    Phred average: 744.7
    Phred average without failures: 760.6
    Percent failed: 2.1%

ALIGNMENT PROTOCOL
==================

    Quality-trimmed BAC end reads from the file Gcanescens_BES.clipped were
    aligned with LASTZ 1.02.00 using "--chain --gapped --ambiguous=n" and
    filtered by requiring a minimum of 90% coverage and 90% identity; if more
    than two alignments for a read satisfied this criteria, all alignments for
    the read were discarded unless at least one alignment was within
    1,000,000bp of a mate's alignment.

    The resulting alignments are available in Gcanescens_BES.clipped.gff.

ALIGNMENT STATISTICS
====================

    Total Reads

        125,950

    Aligned Reads

        97,315

    Reads having alignments with >= 90% coverage & identity

        19,728

    Reads remaining after filtering those with more than 2 alignments and no
    alignments within a 1,000,000bp window of a mate's alignment

        19,257

    Number of alignments for remaining reads

        25,547

ACKNOWLEDGEMENTS
================
This work was supported by the National Science Foundation under Grant No.
0822258-DFBI.