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Figure 3 | BMC Genetics

Figure 3

From: Genomic complexity of the variable region-containing chitin-binding proteins in amphioxus

Figure 3

Allelic polymorphism across the VCBP2/5 gene cluster. A. Genomic profile (using Gestalt viewer) of BAC 62d19, indicating the location of inverted repeats (IRs) in the context of other genomic features. The top two graphs represent the CpG contrast values (observed/expected) and the G+C percentage (green – below 43%, blue – between 43% and 50%, red – above 50%), both shown as deviations from the regional average. The middle section represents features with directionality: features above the black midline are in the forward strand, while those displayed under the midline are in the reverse strand of the sequence. The various tracks depict interspersed repeats (SINEs in red, LINEs in green, DNA and LTR elements in brown, other repeats in purple), inverted repeats (IRF: blue blocks represent the repeats, diagonal lines connect the corresponding repeats on opposite strands) and gene predictions by GenScan. The bottom section is the sequence scale, in kb. B. Dot plot comparison against the corresponding region from BAC contig 63n5-43b24 (y-axis) reveals extensive haplotype variation (diagonal line breaks), much of which is associated with indel polymorphism. The VCBP2/5 cluster is boxed in B and the center repeat (darkened square in B) is oriented with the corresponding region of the Gestalt genome viewer (A). A large break is highlighted and corresponds to three large inverted repeats (dark blue) within the VCBP2 gene. Note: in order to conserve space, dot plot cropped to reflect area surrounding VCBP genes. C. Calculated polymorphism (SNP; indels count as single base change, see text) across the corresponding region in (A) and (B). The results are summarized as average match, mismatch and mutated over the entire BAC: 87.7% of the aligned nucleotides are identical between the two sequences, but only 7.6% of the aligned nucleotides are different. The discrepancy is due to the presence of gaps. Accounting for mismatched nucleotides, those in front of small gaps, and counting every larger indel (>2 bp) as a single change results in 8.6% mutated between the two sequences. Sequences are shown in same orientation as Figure 1. Matched: number of nucleotides aligned and identical; Mismatched: number of nucleotides aligned, but different; Mutated: combined mutation as insertion, deletion and point mutation where frequency of all mutation divided by sequence length is the "mutated" density.

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