Corey T. Watson1,2,, Karyn Meltz Steinberg3,4,, Tina A. Graves4, Rene L. Warren5, Maika

SUPPLEMENTARY MATERIALS: Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity

Corey T. Watson1,2,*, Karyn Meltz Steinberg3,4,*, Tina A. Graves4, Rene L. Warren5,

Maika Malig3, Jacqueline Schein5, Richard K. Wilson4, Robert A. Holt5, Evan E.

Eichler3,6, Felix Breden1 Supplementary Figure 1. Complex repeat structure revealed within the genome assembly gap of the IGK locus. A self to self pairwise BLAST (blastn) of 51 kb of proximal sequence from the BAC clone CH17-158B1 (AC233264) that extends into the currently unsequenced gap between the IGK proximal and distal V gene regions. The size of the gap was previously estimated to be ~800 kb in size (Brensing-Küppers et al., 1997;

Kawasaki et al., 2001). The results of the BLAST show that the region consists of large structurally complex sequence repeats. Supplementary Figure 2. CHM1 SNP density estimates within the proximity of human autosomal telomeres and centromeres. The fraction of bp within 3 Mb (A) and

1 Mb (B) of telomeres (p and q arms) and centromeres on all 22 human autosomes that are covered by SNPs identified in DNA from the CHM1 hydatidiform mole cell line

(Steinberg et al., in preparation; NCBI BioProject ID: 176729). SNP densities are displayed by chromosome (labelled on x axis) for both telomeres (p and q) and the centromere. The arrows in both panels indicate the q arm of chr14 that harbors IGHV. Supplementary Figure 3. Density of segmental duplications within 1 Mbp of human autosomal telomeres and centromeres. The fraction of bp within 1 Mb of telomeres (p and q arms) and centromeres on all 22 human autosomes that are covered by SDs.

Densities are displayed by chromosome (labelled on x axis) for both telomeres (p and q) and the centromere. The arrows in both panels indicate the q arm of chr14 that harbors

Supplementary Tables (large excel files)

Supplementary Table 1. Allelic differences between CH17 and Kawasaki haplotypes of IGLV

Supplementary Table 2. Allelic differences between CH17 and Kawasaki haplotypes of IGKV

Supplementary Table 3. Novel SNPs in CH17 in IGKV, IGKL and IGHV