Sequencing data processing apparatus and method

Disclosed are a sequencing data processing apparatus, system and method, a computer-readable storage medium, and a method and apparatus for detecting SNP (Single Nucleotide Polymorphism), the sequencing data processing apparatus comprising: a data receiving unit (10) for receiving the sequencing data, wherein the sequencing data comprises a plurality of read pairs with each pair being composed of two reads originating from two locations of one chromosome segment respectively, and each read comprises a gap; a processor (20) for executing a data processing program, wherein executing the data processing program comprises comparing the sequencing data with a reference sequence to obtain a comparison result, and eliminating the gap of each read in the comparison result to obtain a universal comparison result; and at least one storage unit (30) for data storage, wherein the data processing program is comprised.