MEI detection modes.
a) RP signature for of non-reference MEI detection. The RP signature consists of Illumina read pairs spanning into the element from each side of the insertion. The RP event display shows a heterozygous Alu insertion allele on chromosome 22 from the trio pilot dataset. Fragment mapping quality is shown on the vertical scale. Horizontal grey lines show read pairs uniquely mapped at both ends with a mapped fragment length consistent with the sequence library; the blue and red lines are read pairs spanning into an Alu sequence from the 5′ and 3′ ends. The green vertical line is the position of the insertion. Thick black lines near the top show annotated Alu positions. Red and blue reads bracketing annotated elements are characteristic of mapping artifacts that we removed from insertion detection by masking out regions within a fragment length of an annotated element of the same family as the insertion. b) Signature for SR-based insertion detection. Split-mapped 454 reads span into the element sequence. The SR event display shows split reads spanning into an Alu insertion from the 5′ (blue) or the 3′(red) sides. The vertical green line marks the insertion site. Fully mapped 454 reads are shown in gray. Gray reads that span the breakpoint correspond to the reference allele. Note that the mapping quality increases with the length of the split-mapped segment. The red and blue segments overlap by roughly 15 bp in the target site duplication region that brackets the MEI insertion. c) Overlap between non-reference MEI detected by RP and by SR. d) Overlap between detection methods for reference MEI. Of the 23 1000GP deletion call sets, 11 were RP and 4 were SR. Also shown are the relative proportions of events detected by assembly (yellow) and by read depth (gray) both of which had nearly 100% overlap with RP and SR calls. e) RP signature for reference MEI detection. Read pairs with abnormally long mapped fragment lengths (in green) span over an AluYb8 annotation. The event display shows RP evidence for a homozygous reference MEI in chromosome 22 from the trio dataset. The yellow line at the top marks homologous regions from the chimpanzee assembly, with a gap at the precise location of the variant MEI.