contig_1 EST:8 availEST:8 potentialSNP&indel:8 indel:1 goodquality-SNP:6 
contig_1 availEST-without-paralogs:8 unigene:unknown D-value:0.0000 haplotype:3 single-haplotype:0 paralogs:0 real-SNP:8 true-SNP:4 error-SNP:4
contig_5 EST:7 availEST:7 potentialSNP&indel:9 indel:1 goodquality-SNP:6 
contig_5 availEST-without-paralogs:7 unigene:unknown D-value:0.8431 haplotype:3 single-haplotype:0 paralogs:0 real-SNP:9 true-SNP:6 error-SNP:3
contig_6 EST:17 availEST:17 potentialSNP&indel:49 indel:17 goodquality-SNP:46  with 1 tri-allelic potential SNP: 801
contig_6 availEST-without-paralogs:15 unigene:unknown D-value:0.3919 haplotype:9 single-haplotype:2 paralogs:0 real-SNP:46 true-SNP:22 error-SNP:24
contig_8 EST:4 availEST:4 potentialSNP&indel:6 indel:1 goodquality-SNP:5 
contig_8 availEST-without-paralogs:4 unigene:unknown D-value:0.0000 haplotype:4 single-haplotype:4 paralogs:0 real-SNP:6 true-SNP:5 error-SNP:1
contig_12 EST:10 availEST:10 potentialSNP&indel:19 indel:0 goodquality-SNP:13  with 1 tri-allelic potential SNP: 884
contig_12 availEST-without-paralogs:5 unigene:unknown D-value:0.0000 haplotype:7 single-haplotype:5 paralogs:0 real-SNP:6 true-SNP:5 error-SNP:1
contig_13 EST:8 availEST:8 potentialSNP&indel:15 indel:9 goodquality-SNP:12 
contig_13 availEST-without-paralogs:6 unigene:unknown D-value:0.3214 haplotype:5 single-haplotype:2 paralogs:0 real-SNP:12 true-SNP:8 error-SNP:4
contig_15 EST:6 availEST:6 potentialSNP&indel:9 indel:6 goodquality-SNP:3 
contig_15 availEST-without-paralogs:5 unigene:unknown D-value:0.0000 haplotype:3 single-haplotype:1 paralogs:0 real-SNP:7 true-SNP:3 error-SNP:4
contig_16 EST:17 availEST:17 potentialSNP&indel:28 indel:11 goodquality-SNP:20  with 2 tri-allelic potential SNP: 743 799
contig_16 availEST-without-paralogs:13 unigene:unknown D-value:0.7820 haplotype:9 single-haplotype:4 paralogs:0 real-SNP:19 true-SNP:8 error-SNP:11
contig_23 EST:12 availEST:12 potentialSNP&indel:9 indel:4 goodquality-SNP:6 
contig_23 availEST-without-paralogs:11 unigene:unknown D-value:0.4472 haplotype:6 single-haplotype:1 paralogs:0 real-SNP:8 true-SNP:3 error-SNP:5
There are 14 available contigs including 109 ESTs
  Of which, there are 9 contigs with potential SNPs, and include 89 ESTs and 152 potential SNPs
  indel:50 CTcounter:18 AGcounter:26   transition:44
  ATcounter:18 ACcounter:16 CGcounter:4  TGcounter:16  transversion:54
  Total length of total 9 contigs with SNP:10235, and the frequency of all SNP(including InDel) is: 67.3 
  The frequency of transition and transversion SNPs: 104.4 ,the frequency of Indel is:204.7
  including 4 tri-allelic polymorphisms

********good quality SNP ******** 
  SNP with high quality
  CT:13 AG:23  transition:36 
  AT:13 AC:11  TG:12 CG:3 transverstion:39 
  and 40 indelSNP with good quality
  including 2 high tri-allelic polymorphisms
  Total SNP with good-quality:117 
  Total length of total 9 contigs with SNPs:10235, and the frequency of all SNP ( including InDel )in potential orthologs&heterozygous contigs is: 87.5 
  The frequency of potential Indel: 255.9, the frequency of transition and transversion SNPs: 136.5 
  Total 84 inter-snp and 51 intra-snp

 ******** true and good quality SNP******** 
  removed single haplotypes:19  and paralogs:0  total removed EST:19
  total SNP in clusters with single haplotype:121 and removed-SNP:31 total true-SNP:64 total error-SNP :57
  SNP with good quality:
  CT:9 AG:8  transition:17 
  Indel:32 AT:4 AC:4  TG:4 CG:3 transversion:15 
  including 0 high tri-allelic polymorphisms
  total true-SNP with good quality:64 
  Total length of 9 contigs with SNPs : 10235
  The frequency of all SNP ( including InDel ) is: 159.9; SNP per contig: 7.1
  The frequency of potential Indel: 319.8, the frequency of transition and transversion SNPs: 319.8 
  Total 29 snp in fasta

*****haplotypes of major and minor allels in all contigs
major allel:0:28  2  0  0  0  0  
major allel:1:16  23  0  0  0  0  
major allel:2:5  12  0  2  0  0  
major allel:3:3  2  5  3  0  0  
major allel:4:1  9  4  0  0  0  
major allel:5:1  3  2  0  0  0  
*****haplotypes of major and minor allels in all avail contigs
major allel:0:18  2  0  0  0  0  
major allel:1:11  22  0  0  0  0  
major allel:2:4  12  0  2  0  0  
major allel:3:1  2  5  3  0  0  
major allel:4:1  9  4  0  0  0  
major allel:5:1  3  2  0  0  0  
