Table 2 Pangenome graph reference statistics. Segment type indicates which assembly the segments originally come from. For the “Segments used by at least 2 MIKK samples” columns, we defined a segment as being used if its coverage is at least 10% of the average coverage over the HdrR reference segments
From: Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
Segment type | All segments in graph | Segments used by at least 2 MIKK samples | Median segment length | Longest segment | N50 | Median % identity | ||
|---|---|---|---|---|---|---|---|---|
Length (bp) | # segments | Length (bp) | # segments | |||||
HdrR | 734,100,826 | 648,692 | 713,609,808 | 615,564 | 401 | 675,459 | 3000 | NA |
HNI | 103,507,879 | 148,689 | 43,204,187 | 47,854 | 239 | 175,667 | 2003 | 62.9% |
HSOK | 152,043,332 | 100,275 | 49,055,247 | 23,881 | 371 | 236,527 | 5803 | 60.4% |
MIKK | 318,174,656 | 211,836 | 203,539,620 | 161,533 | 559 | 89,792 | 3998 | 73.7% |
All | 1,307,826,693 | 1,109,492 | 1,009,408,862 | 848,832 | 389 | 675,459 | 3342 | NA |