control and test in DE in RNA-seq

[honey]

I have been analyzing the mRNA-seq data using Cuffdiff and has two questions:

1. In case of Differential expression analyis between a control vs test sample, ln fold change is represented as Value2/ Value1 as per the manual of Cufflink. I was wondering Value 1 should be control while Value 2 should be test sample.
From Cufflink manual:
FPKMx 8.01089 FPKM of the gene in sample x
FPKMy 8.551545 FPKM of the gene in sample y
ln(FPKMy/FPKMx) 0.06531 The natural log of the fold change y/x

2. In typical control vs test sample based on Hg19 reference annotation- I get around 36K transcripts (total including no test and test OK) that seems to be little less as expected. Does it seem to be right number?

3. When I combine/ filter combined GTF file with any of isoform.exp file I get
RIC8A chr11:202907-236320 OK chr11 207163 208938 exon 1
RIC8A chr11:202907-236320 OK chr11 209271 209318 exon 2
RIC8A chr11:202907-236320 OK chr11 209407 210000 exon 5

Here the combined GTF provide a location (in red) Chr11 202907-236320 while cufdiff provide exon spanning 207163 208938. What is the first location refer to It is referring to neither gene location nor longest transcript. Any suggestion please.
Thanks

[honey]

Question

Any suggestion please.