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With the Next Generation Sequencing technology rapidly developing its very easy to generate large amount of data at a lost cost.In this project,two hybrids in a semi-glutinous RIL and their parents were sequenced at 30x coverage using Hiseq 2000 system to study the difference between the two hybrids and the genetics traits from their parents which may cause some difference between them.The online genome information of Nipponbare supplying by the University of Michigan was as reference,up to 53.6G clean data had produced from the four gene libraries of these samples.The software of SOAP2 was used for analyzed the SNPs,InDels and SVs among the hybrids and their parents,the number of SNPs and Indels in each chrosome in these samples and the number of synonymous and non-synonymous SNPs in each sample was counted.The numbers of SVs included insertion and deletion among these samples were analyzed by the SOAPsv and also counted,large useful information we obtained from these analyzed.More than 180 genes which involve in rice growth and development character,resistance,yield,amylose biosynthesis and etc al were also analyzed between in these hybrids and their parents.