This work was supported by the National Science Foundation under Grant No. 0822258-DFBI
Name Last modified Size Description
Parent Directory - Gsyndetika_BES.clipped.gff.bz2 2012-08-09 09:30 1.4M Gsyndetika_BES.clipped aligned to G. max Gsyndetika_BES.clipped.bz2 2010-04-26 14:38 34M quality-trimmed Gsyndetika_BES.fasta Gsyndetika_BES.fasta.bz2 2010-04-26 14:38 41M Glycine syndetika BAC-end sequence Gsyndetika_BES.qual.bz2 2010-04-26 14:43 49M quality scores for Gsyndetika_BES.fasta
Glycine syndetika BAC-end sequence from the SoyMap II project ============================================================= CONTENTS ======== Gsyndetika_BES.clipped.bz2 - quality-trimmed Gsyndetika_BES.fasta Gsyndetika_BES.clipped.gff.bz2 - Gsyndetika_BES.clipped aligned to G. max Gsyndetika_BES.fasta.bz2 - Glycine syndetika BAC-end sequence Gsyndetika_BES.qual.bz2 - quality scores for Gsyndetika_BES.fasta README.txt - This README file BAC LIBRARY INFORMATION ======================= SOG AGI constructed library GS_Ba HindIII cut 168kb average insert size 14x genome coverage Complete set 292 plates Sequenced 200 Sequencing stats: Phred20 Reads %ofReads 0- 49 2627 1.7% |X 50- 99 1356 0.9% | 100-149 811 0.5% | 150-199 670 0.4% | 200-249 667 0.4% | 250-299 643 0.4% | 300-349 756 0.5% | 350-399 864 0.6% | 400-449 1135 0.7% | 450-499 1687 1.1% |X 500-549 2800 1.8% |X 550-599 4069 2.6% |X 600-649 5973 3.9% |XX 650-699 10319 6.7% |XXX 700-749 20334 13.2% |XXXXXXX 750-799 36055 23.5% |XXXXXXXXXXXX 800-849 45305 29.5% |XXXXXXXXXXXXXXX 850-899 17019 11.1% |XXXXXX 900-949 510 0.3% | Number of reads: 153,600 Total bases: 142,723,366 Total Phred 20 bases: 112,381,753 Average length: 929.2 Phred average: 731.7 Phred average without failures: 743.0 Percent failed: 1.6% ALIGNMENT PROTOCOL ================== Quality-trimmed BAC end reads from the file Gsyndetika_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 Gsyndetika_BES.clipped.gff. ALIGNMENT STATISTICS ==================== Total Reads 148,982 Aligned Reads 121,361 Reads having alignments with >= 90% coverage & identity 32,936 Reads remaining after filtering those with more than 2 alignments and no alignments within a 1,000,000bp window of a mate's alignment 32,328 Number of alignments for remaining reads 43,403 ACKNOWLEDGEMENTS ================ This work was supported by the National Science Foundation under Grant No. 0822258-DFBI.