The Whole genome alignment between two genome assemblies were stored using a "bed" like format:
    - Column 1: Reference Genome Chromosome
    - Column 2: Reference Genome start position
    - Column 3: Reference Genome end position
    - Column 4: a json record of the query genome alignment info, with format of:
                id:ALN_ID{
                    chr:"QUERY_CHR",
                    start:QUERY_START,
                    stop:QUERY_STOP,
                    strand:"QUERY_STRAND",
                    targetseq:"REFERENCE_SEQUENCE",
                    queryseq:"QUERY_SEQUENCE"
                }
For example:

chr0    23550   24109   id:410103,genomealign:{chr:"B73V4_ctg92",start:14098,stop:14657,strand:"+",targetseq:"TCAACACCAACACGAGCACATCTACACCAGCAGCACCTTCTCTAGCCCAGGCGCCACCCCTTCCACCTGGGCCAGTGACTCGGGCCCGTGCAAGAGAATTGAACTACATCATGTTGTTAAAGAACGAAGGCCCGGAAGAATAGACGACCAGCCCAATTGCGGCCCATAATGGACGACCTAGGGTTGGCCGCTCCTAGGGGCTGCGCCCCCTCTCTATTTATTCAGGAGCTGCGCCTCCTTTATTTTCCGAGTTTTGTTTTACGTTAGCCTTAGCTACTCTCGAACACGCGCAAATCTGCGCTGTCTTCGTGTATTCAGAACTCCACCCTCGAGTAATAGATTAGATTGCTCGCATCTTGTTCTTGTTCGTTCTTCGATTGCGCACAGGAAACGATCTTCGTGATCAGGCCGATCTCGCATCAGCAAGGTCGGTAACCACAGGGAGTTGGTTCAGCGATTGCATTGGCGCCTCGGGCTTGCTCGTCGTAGTCGGATCGCAAGGGTCATCTTCCGCCAAATCGGAATTATCTCTACTCGCCGAAAGATCGGGCACCTCAGCT",queryseq:"TCAACACCAACACGAGCACATCTACACCAGCAGCACCTTCTCCAGCCCAGGCGCCACCCCTTCCACCTGGGCCAGTGACTCGGGCCCGTGCAAGAGAATTGAACTACATCATGTTGTTAAAGAACGAAGGCCCGGAAGAATAGACGACCAGCCCAATTGCGGCCCATAATGGACGACCTAGGGTTGGCCGCCCCTAGGGGCTGCGCCCCCTCTCTATTTATTCAGGAGCTGCGCCTCCTTTATTTGCTGAGTTTTGTTTTACGTTAGCCTTAGCTACTCTCGAACACGCGCAAATCTGCGTTGTCTTCGTGTATTCAGAACTCCACCCTCGAGTAATAGATTAGATTGCTCGCATCTTGTTCTTGTTCGTTCTTCGATTGCGCACAGGAAACGATCTTCGTGATCAGGCCGATCTCGCATCAGCAAGGTCGGTAACCACAGGGAGTTGGTTCAGCGATTGCATTGGCGCCTCGGGCTTGCTCGTCGTAGTCGGATCGCAAGGGTCATCTTCCGCCAAATCGGAATTATCTCTACTCGCCGAAAGATCGGGCACCTCAGCT"}