Clade A (European-type) / clade B (North-American-type) evidence on universal bins (5 uMb windows of a consensus order of
single-copy ApeKI-tag anchors shared by the 13 v5 panel haplotypes). Every sample row is drawn the same way: one tile per universal bin, same
height, whatever the assay; the source resolution is stated in each panel header (all cohorts were called on 5 Mb 21110M bins; Apollo from
3 x 100 kb windows per bin). Choose the reference the calls were made on (2026-10-13: only references with calls are offered; the lifted-over display frames were removed).
Status: tentative (2026-09-29).
2026-09-30 layers (sync/2026-09-30/phased_parents_switch_concordance): each cross parent has two phased haplotype lanes (h1/h2; phasing method and
confidence in the label and hover); faint vertical lines through the progeny rows mark the parents' A↔B switch points (purple = mother, teal = father);
each progeny row has a per-chromosome badge: a consistent (one maternal + one paternal homolog),
b recombinant (number = crossovers; ticks on the row), c inconsistent.
The transmission track is the B-allele frequency among progeny with the per-bin expectation from the two parents' genotypes.
Datasets
A / AAABB / BBAAB (triploid)ABB (triploid)a / b haplotype call via 21110M onlyno callsplit / not liftedterminal zoneclick a panel header to collapse / expand; click a sample row for its evidence detailbreakpoint marks (optional track): grey tick = state change, magenta = direct AA↔BB
Phase lanes (parents): full colour = assembly-phased or progeny-linked (support ≥ 0.9); paler = progeny-linked 0.8–0.9; palest = unlinked AB bin (orientation arbitrary)mother / father: switch-point guide lines and crossover ticksBadges: (a) consistent (b) recombinant (c) inconsistent not determinableTransmission: - - - expected (parents) — observed mean 95% CI
Badges on row labels (sex, trace Y, OSU tags, graded paternity): hover one for its evidence, or see the badge pageSex chromosomes (track "Sex-aware ChrX + ChrY", on by default):ChrX: full-height tile = diploid (females; PAR in males); half-height tile = haploid male X; black tick on a male row = his PAR/MSY boundary (X 234.0 Mb lupulus-type Y, 240.8 Mb American-type Y)ChrY (MSY, 21110M 0–132 Mb; haploid; male-specific region; unverified placement): lupulus-type Y (L) American-type Y (Am) absent (female) male call without clean Y reads
Reference: the calls drawn are the calls made on the selected reference (21110M = the served atlas calls, all cohorts; any other reference = calls re-made on that reference, drawn only for the plants aligned to it, in its own bins). The lifted-over display frames were removed on 2026-10-13.
Diagnostic-site ticks (height = read depth, capped 16):A-allele reads onlyB-allele reads onlyboth allelesno coverage (density per 250 kb)Bar above the ticks = the call of each calling bin at the selected resolution, drawn in the same frame and orientation as the rows; white = no call.
The calls and read counts are from the 21110M alignments (site-level detail exists on 21110M only).
For each chromosome: the mother's and father's two phased lanes (h1/h2), the lane this plant inherited from each parent along the
chromosome (exact minimum-crossover search; no smoothing), the state that combination predicts, and the observed calls. Crossover intervals are shaded
(purple = maternal, teal = paternal); red ticks under the observed row = bins at fault (mismatch runs of ≥ 2 called bins); orange ticks = isolated single-bin mismatches (possible call error).
Blocks (table view, current chromosome)Panels and sample counts