Fig. 6

Displayed is a summary of the evolution of junctions from the GENCODE annotation of hg19 through its 18 releases compared to the evolution of confidently called junctions called across the SRA. Every junction considered here is “confidently called”—found in at least 20 reads across the SRA samples we analyzed. a shows that most junctions (80.0%) annotated by GENCODE first appeared in the first release. b shows that junctions in GENCODE tend to have early discovery dates. This is also evident from c, which shows that while only 20.3% of junctions are discovered by late January 2010, almost three-quarters of junctions appearing in at least one GENCODE release are discovered by the same date. Also shown in b is how junctions first appearing in GENCODE’s first release have noticeably earlier discovery dates than junctions first appearing in later releases. This is due to how junctions first appearing in GENCODE’s first release tend to be found in many more samples (median = 5825) than junctions first appearing in later releases (median = 602 samples), as shown in d. In every box plot, the red diamond corresponds to the median, and the blue triangle corresponds to the mean