This work was supported by the National Science Foundation under Grant No. 0822258-DFBI
Name Last modified Size Description
Parent Directory - Gsoja_BES.clipped.gff.bz2 2012-08-09 09:39 4.9M Gsoja_BES.clipped aligned to G. max Gsoja_BES.clipped.bz2 2010-02-16 17:05 41M quality-trimmed Gsoja_BES.fasta Gsoja_BES.fasta.bz2 2010-02-16 17:02 50M Glycine soja BAC-end sequence Gsoja_BES.qual.bz2 2010-02-16 17:04 63M quality scores for Gsoja_BES.fasta
Glycine soja BAC-end sequence from the SoyMap II project ============================================================= CONTENTS ======== Gsoja_BES.clipped.bz2 - quality-trimmed Gsoja_BES.fasta Gsoja_BES.clipped.gff.bz2 - Gsoja_BES.clipped aligned to G. max Gsoja_BES.fasta.bz2 - Glycine soja BAC-end sequence Gsoja_BES.qual.bz2 - quality scores for Gsoja_BES.fasta README.txt - This README file BAC LIBRARY INFORMATION ======================= SOD AGI constructed library GSS_Ba HindIII cut 150kb average insert size 12x genome coverage Complete set 240 plates Sequenced 240 Sequencing stats: Phred20 Reads %ofReads 0- 49 2486 1.3% |X 50- 99 1282 0.7% | 100-149 905 0.5% | 150-199 839 0.5% | 200-249 904 0.5% | 250-299 930 0.5% | 300-349 1066 0.6% | 350-399 1411 0.8% | 400-449 1786 1.0% | 450-499 2362 1.3% |X 500-549 3422 1.9% |X 550-599 4810 2.6% |X 600-649 6780 3.7% |XX 650-699 11547 6.3% |XXX 700-749 24218 13.1% |XXXXXXX 750-799 39229 21.3% |XXXXXXXXXXX 800-849 46936 25.5% |XXXXXXXXXXXXX 850-899 29748 16.1% |XXXXXXXX 900-949 3640 2.0% |X 950-999 19 0.0% | Number of reads: 184,320 Total bases: 178,074,447 Total Phred 20 bases: 136,188,824 Average length: 966.1 Phred average: 738.9 Phred average without failures: 747.9 Percent failed: 1.2% ALIGNMENT PROTOCOL ================== Quality-trimmed BAC end reads from the file Gsoja_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 mate-pairing resulted, in which case all non-paired alignments for the BES were discarded. Mates were paired if and only if the resulting BAC insert spanned a region between 5,000bp and 300,000bp, and there was only one such pairing possible for each mate. The resulting alignments are available in Gsoja_BES.clipped.gff. ALIGNMENT STATISTICS ==================== Total Reads 180,099 Aligned Reads 179,987 Reads having alignments with >= 90% coverage & identity 171,264 Reads remaining after filtering those with more than 2 alignments and no alignments within a 1,000,000bp window of a mate's alignment 144,998 Number of alignments for remaining reads 176,545 ACKNOWLEDGEMENTS ================ This work was supported by the National Science Foundation under Grant No. 0822258-DFBI.