This work was supported by the National Science Foundation under Grant No. 0822258-DFBI
Name Last modified Size Description
Parent Directory - Gstenophita_BES.clipped.gff.bz2 2012-08-08 16:51 687K Gstenophita_BES.clipped aligned to G. max Gstenophita_BES.clipped.bz2 2010-04-18 11:14 21M quality-trimmed Gstenophita_BES.fasta Gstenophita_BES.fasta.bz2 2010-04-18 11:15 27M Glycine stenophita BAC-end sequence Gstenophita_BES.qual.bz2 2010-04-18 11:15 35M quality scores for Gstenophita_BES.fasta
Glycine stenophita BAC-end sequence from the SoyMap II project ============================================================= CONTENTS ======== Gstenophita_BES.clipped.bz2 - quality-trimmed Gstenophita_BES.fasta Gstenophita_BES.clipped.gff.bz2 - Gstenophita_BES.clipped aligned to G. max Gstenophita_BES.fasta.bz2 - Glycine stenophita BAC-end sequence Gstenophita_BES.qual.bz2 - quality scores for Gstenophita_BES.fasta README.txt - This README file BAC LIBRARY INFORMATION ======================= SOK AGI constructed library GS_ABa HindIII cut 149kb average insert size 12x genome coverage Complete set 175 plates Sequencing 120 Sequencing stats: Phred20 Reads %ofReads 0- 49 3849 4.2% |XX 50- 99 1026 1.1% |X 100-149 682 0.7% | 150-199 565 0.6% | 200-249 531 0.6% | 250-299 474 0.5% | 300-349 524 0.6% | 350-399 606 0.7% | 400-449 689 0.7% | 450-499 893 1.0% | 500-549 1223 1.3% |X 550-599 1851 2.0% |X 600-649 3049 3.3% |XX 650-699 5827 6.3% |XXX 700-749 11198 12.2% |XXXXXX 750-799 19290 20.9% |XXXXXXXXXX 800-849 23664 25.7% |XXXXXXXXXXXXX 850-899 14484 15.7% |XXXXXXXX 900-949 1731 1.9% |X 950-999 4 0.0% | Number of reads: 92,160 Total bases: 94,599,393 Total Phred 20 bases: 66,041,381 Average length: 1026.5 Phred average: 716.6 Phred average without failures: 745.2 Percent failed: 3.9% ALIGNMENT PROTOCOL ================== Quality-trimmed BAC end reads from the file Gstenophita_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 Gstenophita_BES.clipped.gff. ALIGNMENT STATISTICS ==================== Total Reads 86,958 Aligned Reads 71,263 Reads having alignments with >= 90% coverage & identity 16,078 Reads remaining after filtering those with more than 2 alignments and no alignments within a 1,000,000bp window of a mate's alignment 15,749 Number of alignments for remaining reads 20,838 ACKNOWLEDGEMENTS ================ This work was supported by the National Science Foundation under Grant No. 0822258-DFBI.