Badge index: row-label badges in the introgression atlas
Status: TENTATIVE · 2026-10-08 · counts taken from the served data file sexchrom/atlas_sexchrom.json (2,264 sample records) and viewer_tags.tsv.
A badge is a small coloured token drawn in front of a sample name on the atlas row label. It marks a plant whose record carries a verified measurement that disagrees with, or adds to, what the published metadata or the default lanes show. Badges are rendered as CSS pseudo-content, so the label text itself stays the sample name and searches on names are unaffected; each badge type also adds a filter token (listed below) so the rows can be selected. Every badge rests on a dated, tentative analysis: it records what was measured and how, not a settled biological fact, and the evidence page linked from each entry says what the measurement can and cannot show.
1. Sex-call disagreement badge
As shown: sex F, sex M, sex XXY+Y or sex Xint+Y; pale red background, dark red text. Hover: verified sex, the published or BioSample label, and the line "DISAGREES: …". Filter token sex:disagree (also vsex:f, vsex:m, vsex:xxy+y, vsex:xint+y for the verified class).
Meaning. The plant's sex as verified from its reads differs from the label it was deposited with (BioSample sex for OSU; the published 21110M male-specific-Y depth call for Cascade × LB_male and Saaz × HL1012). The X and Y lanes follow the verified sex; the badge keeps the disagreement visible rather than silently overwriting the label.
How decided. Two read-based measurements made on all reads including unmapped ones (2026-10-04, extended to the other crosses 2026-10-05): X dosage, the GBS depth at 4,511 X-specific sites (ChrX < 234.0 Mb) divided by depth at 9,081 Chr03 sites, cohort-normalised with 200 site-bootstrap intervals, bimodal with an empty gap between one-X (≤ 0.65) and two-X (≥ 0.85) plants; and male-specific 31-mers from the four assembled Y chromosomes (HL1012, M21_H1, MN1421_h1, MN586_h1) with the mother's own k-mers removed, which also give the Y lineage (L or Am). A plant is badged when the verified class differs from the label. For Saaz the PI asked (2026-10-08) that the four disagreements be kept as disagreements rather than resolved, since the depth caller places them between the female and male rates.
Counts. OSU 2022005: 128 of 369 (116 BioSample-male seedlings verified female, 5 BioSample-female seedlings verified male, 4 two-X + Am-Y "XXY+Y", 3 intermediate-X + Am-Y "Xint+Y"). Cascade × LB_male: 6 (ERR11608335, -422, -433, -434, -437, -441; -437 is a triploid, -422 is unexplained). Saaz × HL1012: 4 (DRR613202, -213, -254, -332), added 2026-10-08. Total 138.
Status. Tentative. The X test is one reference frame (21110M); the Cascade X test is underpowered (69 of 180 plants X-ambiguous, with 0 contradictions to the Y k-mers).
Evidence: sync/2026-10-04/osu_sex_verification/README.md (OSU, Cascade), sync/2026-10-05/sexchrom_scan_all_crosses/README.md (all crosses), sync/2026-10-08/saaz_sex_badges/PIPELINE.sh (Saaz), annevo_eval/docs/ASSAYS.md addenda 2026-10-08 (depth-based sex calls: valid within a cross with MSY-only depth and a corrected X, not for panels). Evidence page: not yet written.
2. Trace-Y badge
As shown: trY; pale yellow background, brown text. Hover: "trace male signal (Y k-mers Y- (trace))". Filter token sex:trace.
Meaning. A plant verified as two-X female whose reads carry a small but non-zero male-specific Y k-mer signal, far below a son's.
How decided. From the same Y k-mer counts as badge 1: every Y k-mer class is present at a uniform few per cent of a son's level, while X dosage is two-X. For 2022005-004 the signal is 5–9 % of an Am-Y son in every class and the Y is 19058m-type; its autosomes show no detectable 19058m-male admixture, so the source is unresolved (a brother is the most compatible source). In Cascade × LB_male the 12 trace plants carry a 1–4 % L-Y signal, and the multi-cross scan found the trace fractions match sibling-mixture fractions. The record treats these as small DNA admixtures, not as divergent Y chromosomes.
Counts. Cascade × LB_male 12; OSU 2022005 1 (2022005-004). Total 13. (The 2026-10-05 scan also lists trace or low-Y plants in Zenith x 21058M 10, Wye 2, Saaz 1, Apollo 1; these are not yet badged in the atlas.)
Status. Tentative; a flag, not a sex call.
Evidence: sync/2026-10-04/osu_sex_verification/README.md (Test 3), sync/2026-10-05/sexchrom_scan_all_crosses/README.md (traceY_vs_sibling_mixture.tsv). Evidence page: not yet written.
3. Purple tag badges (OSU anomalous-seedling dossier)
As shown: the tag label text (e.g. L-Y son, father not 19058m); pale purple background, dark purple text; the badge is a link to the dossier PDF (docs/OSU_anomalous_seedlings_dossier.pdf). Hover: group, short evidence, verdict. Filter tokens tag:<label> and group:<group>; preset ?preset=sex_tags.
Meaning. The plant is one of the 79 OSU 2022005 seedlings written up in the anomalous-seedling dossier of 2026-10-04. Six groups, each with its own evidence:
| group | badge text | n | basis (from the dossier) |
|---|---|---|---|
a_LY_son |
L-Y son, father not 19058m | 19 | one X by dosage + L-type Y (19058m carries an Am-Y); paternal flip 0.155–0.29 vs reference 0.05; OH vs 19058m 0.09–0.26 vs 0.04; maternal side Cascade-consistent |
b_XXY_like |
two X + full Am-Y (XXY-like) | 4 | two-X dosage with the paternal X allele present, plus a full 19058m-type Am-Y (0.79–1.17 of a son); autosomes diploid Cascade × 19058m; a mixture cannot give both |
c_triploid_like |
3 genome copies, 2 from 19058m (XXY triploid-like) | 2 | both 19058m homologs at about 1/3 each across the autosomes, maternal about 1/3, X 0.72, Y 0.5–0.7 of a son, KING to 19058m 0.40; not separable from a fixed 2:1 mix of exactly the father's genome |
c_other_father |
Am-Y son of another father (MN1421-type Y) | 1 | 2022005-320: Am-Y of the MN1421 type while 19058m is MN586 type; paternal alleles not 19058m's |
d_trace_AmY |
daughter with ~5 % Am-Y trace | 1 | 2022005-004; see badge 2 |
np_other_father |
paternity not 19058m | 52 | 48 daughters and 4 Am-Y sons passing the paternity rule (flip > 0.12 and OH > 0.06); see badge 4 |
Counts. OSU 2022005 only: 79 tags on 79 seedlings.
Status. Tentative; the dossier states that nothing in it is a karyotype, and that the triploid-like call needs flow cytometry or a re-extraction to settle.
Evidence: /data/hop_data/osu_anomalous_seedlings/README.md, viewer_tags.tsv, dossier/OSU_anomalous_seedlings_dossier.pdf; for the two paternity groups also osu_paternity.html.
4. Paternity badge: "father is not 19058m" (OSU 2022005)
As shown (since 2026-10-08): a graded row badge father≠19058m · <grade> on 73 OSU seedlings (the 72 flagged + 1 possible); hover it and choose See evidence to open osu_paternity.html for that seedling. Before 2026-10-08 there was no visible badge: the 72 seedlings carried only a hover line "paternity ≠ 19058m (tentative)", the filter token paternity:not-19058m and the preset ?preset=not_19058m; 71 of them are also visible through purple tags (a_LY_son 19 + c_other_father 1 + np_other_father 52 = 72; the 52-tag group and the 72-token set were built from the same rule).
Badge hover: the grade's statistics, e.g. strong · Y: L-type · OH 0.095 [0.081–0.110] (ref ≤ 0.062, 4,699 sites) · flip 0.20 [0.18–0.23] (ref ≤ 0.107) · 14 blocks / 6 autosomes.
Meaning. The seedling's paternal alleles are not consistent with 19058m as father. The badge does not name another father.
How decided. The original flag (2026-10-04) is a point-estimate rule on two autosomal statistics: paternal flip rate > 0.12 (how often consecutive informative sites switch between the two phased 19058m homologs) and opposite-homozygote rate versus 19058m > 0.06 (sites where the seedling has zero reads of 19058m's homozygous allele), with the two triploid-like seedlings removed by hand. The 2026-10-08 audit added a declared reference set of 290 19058m-consistent seedlings, 5-Mb block-bootstrap intervals (2,000 replicates), leave-one-out reference 99th percentiles (OH 0.062, flip 0.107), an independent Y-lineage line, and a per-block test of whether the evidence is spread over the genome. Grades: strong (Y) when the Y lineage alone excludes 19058m; strong (autosomal) when both interval lower bounds clear the reference 99th percentile on ≥ 3 autosomes; moderate when one does; possible for an unflagged seedling that passes the interval rules. Controls: 2/290 reference seedlings grade moderate under the declared rule (1/290 under the replacement block test); a wrong-father control shows the OH arm alone has 18–80 % sensitivity, so the set is probably a minimum.
Counts. OSU 2022005: 72 flagged of 369 = strong (Y) 20 (19 L-Y sons + 2022005-320), strong (autosomal) 47 (43 daughters + 4 Am-Y sons), moderate 5 (all daughters: 2022005-086, -230, -243, -362, -364), weak 0; plus possible 1 (2022005-164, unflagged). No other cohort carries this badge.
Status. Tentative. The reference set is defined by the flag it audits; the per-block test in use replaced a declared one that failed its control; parent genotypes are single GBS libraries.
Evidence: osu_paternity.html (this atlas) · sync/2026-10-08/osu_paternity_uncertainty/README.md and tables/.
5. Retired: "47" badge (Zenith x 21058M 47 of interest)
As shown (formerly): 47; yellow background, black text; hover "Zenith x 21058M 47 of interest: whole-chromosome AB where both parents are AA on …". The code path remains in the viewer but the set it reads is empty since 2026-10-07 (PI decision to remove the Zenith x 21058M 47 tags), so no row shows it.
Counts. 0 rows in every cohort.
Evidence page: not applicable (retired).
Notes on counting
- Badge counts come from the served JSON fields:
vdis(badge 1),vtr(badge 2),vtag(badge 3),vpat(badge 4). Cohort keys:osu,cascade,saaz. Plants in the other cohorts (Zenith x 21058M, Wye, Apollo, panels) have no verified-sex record in the JSON and therefore no badge of any type today, even where the 2026-10-05 scan found trace-Y or low-Y plants. - The verified-sex record of 2026-10-04 reported 134 sex-disagreement rows (128 OSU + 6 Cascade); the 4 Saaz rows added 2026-10-08 bring it to 138.
- The atlas test suites that check these badges (
v05_verified_sex_test.py, 30/30 on :8900) are run only when the PI asks.
Badge catalogue
Generated from the atlas data at build time. Counts = samples (tags: tag instances) carrying the badge.
| Badge | Meaning | n | Source | Evidence |
|---|---|---|---|---|
| father≠19058m · strong | Graded paternity (OSU 2022005) The seedling’s SNP evidence says its father is not 19058m. Grade strong / moderate from 5-Mb block-bootstrap intervals against 290 reference seedlings; possible = not flagged by the original rule but passing the interval rules. Grades: strong 67, moderate 5, possible 1 | 73 | OSU paternity audit 2026-10-08 (per_seedling_paternity_evidence.tsv) | evidence page |
| sex F | Verified sex disagrees with the label Verified sex (X dosage + Y k-mers, 2026-10-04) disagrees with the BioSample / published sex label. | 138 | osu_sex_verification (2026-10-04) | this page |
| trY | Trace Y signal A trace of Y-specific k-mers or reads in a plant called female (or a male call without clean Y reads). | 13 | osu_sex_verification (2026-10-04) | this page |
| tag | OSU anomaly tag One of the OSU 2022005 sex-chromosome / paternity anomaly classes (below). The tag badge itself links to the anomaly dossier. | 79 | osu_anomalous_seedlings viewer_tags.tsv | this page |
| 47 | Zenith x 21058M 47 of interest (retired) Whole-chromosome AB where both parents are AA (T12c). Removed from the viewer on 2026-10-07 at the PI’s request; listed for completeness. | 0 | T12c | this page |
Not row-label badges: the per-chromosome concordance marks a / b / c drawn on progeny rows (see the atlas legend).