This work was supported by the National Science Foundation under Grant No. 0822258-DFBI
Name Last modified Size Description
Parent Directory - Gfalcata_BES.qual.bz2 2010-10-29 09:03 50M quality scores for Gfalcata_BES.fasta Gfalcata_BES.fasta.bz2 2010-10-29 09:04 38M Glycine falcata BAC-end sequence Gfalcata_BES.clipped.gff.bz2 2012-08-08 16:46 728K Gfalcata_BES.clipped aligned to G. max Gfalcata_BES.clipped.bz2 2010-10-28 15:32 31M quality-trimmed Gfalcata_BES.fasta
Glycine falcata BAC-end sequence from the SoyMap II project ============================================================= CONTENTS ======== Gfalcata_BES.clipped.bz2 - quality-trimmed Gfalcata_BES.fasta Gfalcata_BES.clipped.gff.bz2 - Gfalcata_BES.clipped aligned to G. max Gfalcata_BES.fasta.bz2 - Glycine falcata BAC-end sequence Gfalcata_BES.qual.bz2 - quality scores for Gfalcata_BES.fasta README.txt - This README file BAC LIBRARY INFORMATION ======================= SOI AGI constructed library GF_Ba HindIII cut 146kb average insert size 12x genome coverage Complete set 283 plates Sequenced 190 Sequencing stats: Phred20 Reads %ofReads 0- 49 2078 1.4% |X 50- 99 1069 0.7% | 100-149 602 0.4% | 150-199 602 0.4% | 200-249 612 0.4% | 250-299 781 0.5% | 300-349 906 0.6% | 350-399 1018 0.7% | 400-449 1230 0.8% | 450-499 1645 1.1% |X 500-549 2306 1.6% |X 550-599 3634 2.5% |X 600-649 6445 4.4% |XX 650-699 12120 8.3% |XXXX 700-749 22358 15.3% |XXXXXXXX 750-799 35690 24.5% |XXXXXXXXXXXX 800-849 38175 26.2% |XXXXXXXXXXXXX 850-899 13861 9.5% |XXXXX 900-949 786 0.5% | 950-999 2 0.0% | Number of reads: 145,920 Total bases: 138,901,523 Total Phred 20 bases: 106,277,030 Average length: 951.9 Phred average: 728.3 Phred average without failures: 737.6 Percent failed: 1.3% ALIGNMENT PROTOCOL ================== Quality-trimmed BAC end reads from the file Gfalcata_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 Gfalcata_BES.clipped.gff. ALIGNMENT STATISTICS ==================== Total Reads 142,489 Aligned Reads 119,176 Reads having alignments with >= 90% coverage & identity 16,909 Reads remaining after filtering those with more than 2 alignments and no alignments within a 1,000,000bp window of a mate's alignment 16,521 Number of alignments for remaining reads 22,013 ACKNOWLEDGEMENTS ================ This work was supported by the National Science Foundation under Grant No. 0822258-DFBI.