Mean r2, a measure of nonindependence between segregating variants, is generally low between pairs of variants of different types or on different replicons, while the median size and spanned distance of LD groups is less on the megaplasmids than on the chromosome

Variant type or locationMean r2 between
No. ungrouped
No. of LD
Median no. of variants
per LD group
Median LD group
spanned distancea
SNPs only0.0722,0578,3643N/A
PAVs only0.0210,7646322N/A
Between SNPs and PAVs0.03N/A5057N/A
Chromosome SNPs0.247899007173,406
pSymB SNPs0.0513,6714,4783518
pSymA SNPs0.127,5972,91231,063
  • a Spanned distance calculated only for LD groups with SNPs that were all on the same replicon.