how to interpret the output plot

[aaannaw]

Hello,Professor I downloaded the TOGA result file for several species from https://genome.senckenberg.de/download/TOGA/mouse_mm10_reference/Rodentia/. I focused on a gene ENSMUSG00000057170 and the gene is showed loss status in the loss_summ_data.tsv file. The plot for two projections of the gene is showed in one of species: The detailed mutation for the two projections is showed in the geneInactivatingMutations.tsv file, which showed all exons is deleted (masked) and proportion of intact is 0. However, in the ReadeMe, the blue color represented intact status. Thus, the color for the mutation plot is confused for me. I also see the red box, which is represented for loss exon (Mask). Maybe deleted exon with mask or unmask is different? Also, I am confused for the criterion of several status for gene level. The NSMUSG0000001572 gene is depicted to be Missing status and the plot is showed. Perhaps the gene referred as missing is characterized that the proportion of in intact is below the specified value. Also, I see some genes can not be attributed to be any status for several genomes. Could you give me any suggestions and looking forward with your reply. Best wishes! Na Wan