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.clipped.bz2 2011-04-18 11:29 30M quality-trimmed Gcanescens_BES.fasta 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
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.