Fig. 3: Widespread copy number gain and structural mutation.
a, Copy number calls across clam genome, rounded to the nearest integer (black) and unrounded (gray) in 100-kB segments. The healthy clam is a representative individual and the MarBTN sub-lineages are averages of each individual sample from that sub-lineage, which were in close agreement. b, Summary of copy number states across entire genomes for two non-reference healthy clams and MarBTN sub-lineages. Gray lines display copy number summaries for individual samples within each sub-lineage, which are in close agreement. c, Number of SVs in each sample. The reference clam was excluded as one haplotype from that animal was used to build the reference genome and thus does not contain SVs. Values were normalized to the average number of SVs in non-reference healthy clams for each SV type (numbers below SV type labels). P values are from two-sided unequal variance t-test between MarBTN samples (n = 8) and non-reference healthy clams (n = 2). Exact P values are 1.9 × 10−5, 2.9 × 10−2, 1.0 × 10−5 and 8.0 × 10−11, respectively. Labels follow DELLY abbreviations of SV types: BND, translocations; DEL, deletions; DUP, tandem duplications; INV, inversions. Bars indicate means and error bars indicate s.d. d, Size distribution of tandem duplications in each non-reference sample. Dashed line indicates 11 kB. e, Telomere length estimated by TelSeq for each sample. f, Tandem duplicate copies of the mitochondrial D-loop region per sample. Healthy clams are black, MarBTN from PEI are red and MarBTN samples from USA are blue.
