I. NOTES ON SSAHA OUTPUT:

I.1 NOTES 1:

An explanation on the SSAHA hits. Though for some matches, the pid is shown as 75%,
the actual BLAST output would show much more identity as in the following example. 

SSAHA OUTPUT:


>IDB60489-736-1670-splicePos-70          5      60   10.129000001-130000000  579153 579208     FF         56     100.00   [const]
>IDB60489-736-1670-splicePos-70         75     130   10.129000001-130000000  580203 580258     FF         42      75.00   [const]


SEQUENCE:  
>>IDB60489-736-1670-splicePos-70
AGCCATGGCGGTGGAAGGAGGAATGAAGTGTGTCAAGTTTTTGCTCTACGTTCTCCTGCTGGCCTTCTGC
GCCTGTGCAGTGGGATTGATTGCCATTGGTGTAGCGGTTCAGGTTGTCTTGAAGCAGGCCATTACCCATG


BLAST OUTPUT:
>10.129000001-130000000  
            Length = 1,000,000

  Plus Strand HSPs:


Query:      1 AGCCATGGCGGTGGAAGGAGGAATGAAGTGTGTCAAGTTTTTGCTCTACGTTCTCCTGCT 60
              AGCCATGGCGGTGGAAGGAGGAATGAAGTGTGTCAAGTTTTTGCTCTACGTTCTCCTGCT
Sbjct: 579149 AGCCATGGCGGTGGAAGGAGGAATGAAGTGTGTCAAGTTTTTGCTCTACGTTCTCCTGCT 579208

Query:     61 GGCCTTCTGCG  71
              GGCCTTCTGCG  
Sbjct: 579209 GGCCTTCTGCG  579219



Query:     71  GCCTGTGCAGTGGGATTGATTGCCATTGGTGTAGCGGTTCAGGTTGTCTTG 121
               GCCTGTGCAGTGGGATTGAT GCCATTGGTGTAGCGGTTCAGGTTGTCTTG
Sbjct: 580199  GCCTGTGCAGTGGGATTGATCGCCATTGGTGTAGCGGTTCAGGTTGTCTTG 580249

Query:    122 AAGCAGGCCATTACCCATG 140
              AAGCAGGCCATTACCCATG
Sbjct: 580250 AAGCAGGCCATTACCCATG 580268


I.2 NOTES 2:

Checked that the 5p and 3p exonic region match to the same chr contig. For the following cases, they match to the adjacent contigs. However, the conit coordinates indicate that the gene in question crosses-over two contigs.

>IDB63069-2524-3626-splicePos-70         1      70   3.89000001-90000000     999286 999355     FF         56     100.00   [alt]
>IDB63069-2524-3626-splicePos-70        71     139   3.90000001-91000000       846    914      FF         56     100.00   [alt]


>IDB66046-6316-16154-splicePos-70        3      58   4.104000001-105000000   989269 989324     FF         56     100.00   [const]
>IDB66046-6316-16154-splicePos-70       79     134   4.105000001-106000000     379    434      FF         56     100.00   [const]


>IDB63069-2524-3623-splicePos-70         1      70   3.89000001-90000000     999286 999355     FF         56     100.00   [const]
>IDB63069-2524-3623-splicePos-70        70     139   3.90000001-91000000       845    914      FF         56     100.00   [const]


>IDB64217-10438-18654-splicePos-70       1      70   6.5000001-6000000         939   1008      RF         70     100.00   [const]
>IDB64217-10438-18654-splicePos-70      72     127   6.4000001-5000000       989619 989674     RF         56     100.00   [const]


I.3 NOTES 3:

Checked that all splice junctions from one IDB entry match to the same chr region. There are few entries which come from adjacent contigs - the gene in each of these cases crosses-over the adjacent contigs.


>IDB64181-12784-17724-splicePos-70      10      65   5.14000001-15000000     991453 991508     FF         56     100.00   [const]
>IDB64181-12784-17724-splicePos-70      77     132   5.14000001-15000000     997165 997220     FF         56     100.00   [const]


>IDB64181-26620-40192-splicePos-69       7      62   5.15000001-16000000      3151   3206      FF         56     100.00   [const]
>IDB64181-26620-40192-splicePos-69      69     138   5.15000001-16000000     18495  18564      FF         70     100.00   [const]

II. NOTES ON BLAST OUTPUT:

Some of the splice junctions, for which SSAHA did not show matches to both the 5p and 3p exonic regions, showed up good matches when BLAST was used. They are listed in the data file under a separate section.

Some of the matches are not very good (> 95% or so). They may be attributed to sequence quality issues. Such entries are appropriated annotated in the data set.


III. Those splice junctions that did not pass through either SSAHA or BLAST checks, are listed in a separate data file. For some of the splice junctions, either the 5p or the 3p exonic region showed good match with the mouse genome region. For some, the 5p and 3p exonic regions matched as a long contiguous match. FOr some, the matches were either weak or not present at all. Whereever there was a match (either in the 5p or 3p or as a long contiguous match), the mapping was to the same chr region with which other related splice junctions of the gene mapped to.