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ADMIXTURE K:ADMIXTURE K： Black ★/◆ = query · yellow ◆ = pinned sample黑色★/◆=查询样本 · 黄色◆=已钉住样本
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Panel面板
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Query查询
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K8 dominantK8 主组分
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Mean depth平均深度
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Panel call%面板分型率
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PC1–PC3PC1–PC3
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PCA methodPCA 方法
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Identical完全相同
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PO亲子

Sample validity样本有效性 Query-derived查询样本来源

How to read. Start with the report identity, artifact provenance, method coverage, QC, and damage availability before interpreting placement or panel context.
怎么看：先确认报告身份、产物溯源、方法覆盖、质控和损伤信息，再解释样本定位或 panel 背景。

Conclusions结论

How to read. Auto-written takeaways from the tables and plots below. Black ★/◆ is this query; yellow ◆ is a sample you pin by clicking a point, bar, or tree tip.
怎么看：本页对各图/表的自动摘要。黑色★/◆是本查询样本；在图上点击可钉住一个对照样本（黄色◆）。
Interaction: click a point/bar/tip to pin the sample. Black ★/◆ identifies the query; yellow ◆ identifies the pinned sample.
交互：点击点/柱/叶即可钉住样本。黑色★/◆是查询样本；黄色◆是钉住的对照。

    Query snapshot样本速览

    How to read. This sample’s ADMIXTURE K=8 after projection onto the 2449 model. The largest slice is the component it most resembles.
    怎么看：本样本投影到 2449 模型后的 K=8 组成。最大的一块就是最像的组分。
    Passport: filled only if this exact ID is in the 2449 panel (Dong et al. 2023 · VIVC).
    护照信息：仅当该精确 ID 在 2449 面板中时填写 （Dong 等 2023 · VIVC）。

    K=8 compositionK=8 组成

    Metadata元数据

    4K class counts4K 类别计数

    Capture QC捕获质控

    How to read. Two calling rates are not the same. Panel calling rate (highlighted) = called genotypes ÷ 167,433 chip sites — sites never written to the VCF count as failure. VCF-site calling rate = called ÷ sites in this VCF (usually ~100% once a site is written; not capture success). Depth includes zeros; median 0× means more than half the chip has no covering read.
    怎么看：两个分型率不是一回事。 Panel calling rate（高亮）= 已分型 ÷ 167,433 芯片位点（没写进 VCF 的位点也算失败）。 VCF-site calling rate = 已分型 ÷ 本 VCF 位点（位点一旦写出通常接近 100%，不能当捕获成功率）。 深度含 0；中位深度 0× 表示一半以上芯片位点没有覆盖 reads。

    Damage损伤

    How to read. mapDamage2 misincorporation (Ginolhac et al. 2011; Jónsson et al. 2013). Left: from the 5′ end, red = C→T. Right: from the 3′ end (axis reversed so the terminus is on the right), blue = G→A. Grey = other substitutions. Ancient DNA: both termini high, falling inward. The bar plot is the fragment-length histogram from the BAM.
    怎么看：mapDamage2 误掺入 (Ginolhac et al. 2011； Jónsson et al. 2013)。 左：从 5′ 起，红 = C→T。右：从 3′ 起（坐标反向，末端在右侧），蓝 = G→A。灰 = 其他替换。 古 DNA：两端升高、向内下降。柱图是 BAM 片段长度分布。

    Identity & placement身份与定位 Query vs 2449 panel查询样本 vs 2449 面板

    How to read. Identity screens compare this query with the 4K reference set; clone/PO, IBS, KING, and nearest-reference results are query-versus-panel evidence.
    怎么看：身份筛查把本查询与 4K 参考集比较；clone/亲子、IBS、KING 和最近参考样本都属于查询与 panel 的比较证据。

    Clone + PO list克隆与亲子列表

    How to use. The kinship rule and relationship options sit above the graph. Update refreshes this list together with that graph. Other sections stay on the active query. Click a panel row to pin that ref.
    怎么用：亲缘规则和关系选项在关系图上方。点更新后，本列表和那张图一起换。其他板块仍跟着当前查询样本。点面板那一行即可钉住对照。
    Italy 4K screen: Identical + Parent-Offspring. Click a row to pin.
    意大利 4K 筛查：完全相同 + 亲子。点一行即可钉住。

    IBS neighbors + Kinship近邻与亲缘

    How to read. Ranked 4K IBS neighbors and KING kinship. Click a ref ID to pin it on the ancestry plots.
    怎么看：4K IBS 近邻和 KING 亲缘排序。点对照 ID 可钉到祖源图上。
    Top 4K IBS rows and kinship ranking. Click ref to pin on plots.
    4K IBS 近邻行和亲缘排序。点对照即可钉到图上。

    IBS topIBS 近邻

    Kinship top亲缘

    Population placement群体定位 Query vs 2449 panel查询样本 vs 2449 面板

    How to read. PCA, ADMIXTURE, and the NJ tree show where this query sits relative to the 2449 panel. Panel summaries remain panel context; the query marker is a projection or observed genotype.
    怎么看：PCA、ADMIXTURE 和 NJ 树显示本查询相对 2449 panel 的位置。panel 汇总只是 panel 背景；查询标记是投影或实际基因型。

    PCAPCA

    How to read. The 2449 cloud uses frozen GCTA64 GRM-PCA reference axes on 153,483 non-GWAS chip sites (Yang et al. 2011; Vitis autosomes = 19). This query is least-squares projected onto those axes (Patterson et al. 2006). 2D (left) and 3D (right) use square canvases. PC2 is fixed at −0.01…0.01; other axes follow the data min/max. Points outside the PC2 window are not shown. Switch PC1–PC2 / PC1–PC3 / PC2–PC3. Click a point to pin. Black ★/◆ = query; yellow ◆ = pinned.
    怎么看：2449 点云使用冻结的 GCTA64 GRM-PCA 参考坐标轴（153,483 个非 GWAS 芯片位点；Yang 等 2011）。本查询样本以最小二乘投影到这些轴上（Patterson 等 2006）。 二维/三维画布为正方形。PC2 固定 −0.01…0.01；其余轴按数据最小最大值。PC2 窗外的点不显示。可切换 PC 轴；点击钉住。黑★/◆=查询样本，黄◆=钉住的对照。
    PCA: switch PC axes on the left; 3D on the right. Black ★/◆ = query; yellow ◆ = pinned sample. Click a point or tip to pin.
    PCA：左侧切换 PC 轴；右侧为 3D。黑色★/◆=查询样本；黄色◆=钉住对照。点击点或叶即可钉住。
    2D axes:二维坐标轴：

    2D二维

    3D三维

    ADMIXTURE K=2–8ADMIXTURE K=2–8

    How to read. Unsupervised ADMIXTURE at K=2–8 on the 2449 reference (Alexander et al. 2009). Rows share one sample order. Colours are matched K→K+1 by greedy Pearson correlation of Q (label switching). A colour that continues down a column is the same component; a new colour is a split at that K. Palette follows Dong et al. 2023 Fig. 1D. The right-hand column is this sample projected onto the frozen allele-frequency matrix (ADMIXTURE -P), not a new unsupervised run.
    怎么看：2449 参考集上 K=2–8 的无监督 ADMIXTURE。各行样本顺序相同。颜色按相邻 K 的 Q 列 Pearson 相关贪婪匹配（label switching）。一列上下同色=同一组分；新颜色=该 K 发生分裂。右侧一列是本样本投影到冻结的等位基因频率矩阵（ADMIXTURE -P），不是一次新的无监督拟合。
    ADMIXTURE K=2 to K=8

    ADMIXTURE bar (K tabs)ADMIXTURE 柱图（K 标签）

    How to use. One K at a time (top K tabs). Full = whole panel; Compact = even subsample per group. In-panel query uses lookup Q; when Q exists it is a separate right-hand column. Click a bar to pin.
    怎么用：顶部 K 标签一次看一个 K。Full=全 panel；Compact=每组均匀抽。库内样本用 lookup Q；有 Q 时查询样本单独一列。点柱钉住。
    Bar: stacked Q in deterministic report-group order. Default shows the full panel; compact mode samples evenly within groups. In-panel query uses lookup Q at its group position. When Q exists on this strip, the query is a separate right-hand column.
    柱图：按确定的报告分组顺序堆叠 Q。默认显示完整面板；紧凑模式在组内均匀抽样。面板内查询在其组位置使用 lookup Q。当本条带有 Q 时，查询样本单独占右侧一列。
    View:视图：

    NJ TreeNJ 树

    How to use. Neighbor-Joining on IBS genotype-identity (Saitou & Nei 1987). Default view is a centered equal-angle circular phylogram (radius = path length from the root). Switch to rectangular to scroll the ladder. Click a tip to pin.
    怎么用：IBS 基因型距离的 NJ 树（Saitou & Nei 1987）。默认居中等角圆形树（半径=到根的路径长）。可切到矩形阶梯图并在框内滚动。点叶钉住。
    NJ: IBS genotype-identity distance → Neighbor-Joining (Saitou & Nei 1987, doi:10.1093/oxfordjournals.molbev.a040454). All 2449 + query. Circular = equal-angle phylogram; rectangular = rooted ladder (scroll in the 720px box).
    NJ：IBS 基因型同一度距离 → 邻接法 （Saitou & Nei 1987，doi:10.1093/oxfordjournals.molbev.a040454）。全部 2449 + 查询样本。 圆形=等角系统树；矩形=有根阶梯图（在 720px 框内滚动）。
    Layout:布局：

    f3 / f4f3 / f4

    Advanced exploratory allele sharing探索性等位基因共享
    How to read. Reference means are 2449 panel Grp means. The query is one query genotype, not a target population. Missing query sites are excluded per contrast. Top left: outgroup-f3 f3(OUT; query, Grp) — higher = more shared drift with that Grp mean (whiskers = chromosome-block jackknife SE; blue |Z|≥3). Top right: pairwise f4(query, OUT; A, B). Bottom: exploratory f3 f3(query; A, B); it is not a formal qp3Pop/qpDstat/qpAdm/qpGraph result.
    怎么看：参考均值来自 2449 panel 的 Grp。查询是一个基因型，不是目标群体；每个 contrast 排除缺失查询位点。上排左 outgroup-f3 越高越接近该 Grp 均值。上排右 f4 成对柱。下图是探索性 f3，不是正式的 qp3Pop/qpDstat/qpAdm/qpGraph 结果。
    Advanced exploratory allele sharing: Patterson et al. 2012 Genetics 192:1065–1093, https://doi.org/10.1534/genetics.112.145037. Reference means = 2449 panel Grp means; one query genotype, not a target population; missing query sites are excluded per contrast. Tables and tooltips show complete-case n_sites and chromosome-block n_blocks. OUT handling is conditional: when designated OUT is present, its actual n is reported and it is retained even when n < min_n without satisfying min_n; when no designated OUT is available, outgroup-f3/f4 are unavailable. This is not qp3Pop/qpDstat/qpAdm/qpGraph; no formal population-mixture or graph fit is claimed.
    探索性等位基因共享：Patterson 等 2012 Genetics 192:1065–1093， https://doi.org/10.1534/genetics.112.145037。 参考均值=2449 panel 的 Grp 均值；查询是一个基因型，不是目标群体；每个 contrast 排除缺失查询位点。 表格和提示显示完整案例 n_sites 与染色体块 n_blocks。 OUT 处理是条件的：有指定 OUT 时报告实际 n，即使 n < min_n 也保留，但不视为满足 min_n；没有指定 OUT 时，外群 f3/f4 不可用。 这不是 qp3Pop/qpDstat/qpAdm/qpGraph；不声称正式的群体混合或图拟合。

    Exploratory f3 f3(Q; A, B)探索性 f3：f3(Q; A, B)

    Observed in this sample本样品实际观测 Query-derived查询样本来源

    How to read. This section reports query genotypes and per-query predictions. A panel association, trait label, or CV score supplies context; the active evidence is the query call.
    怎么看：本节只报告查询样本的实际基因型和逐样本预测。panel 关联、性状标签或交叉验证分数提供背景；当前证据以查询样本分型为主。

    Query genotype evidence查询样本基因型证据

    Per-query GS predictions本查询 GS 预测 Query-derived查询样本来源

    Panel research context2449 panel 研究背景
    How to read. The following analyses describe the 2449 panel or published reference context. Query genotype overlays are labelled as overlays; panel statistics remain the active computation.
    怎么看：以下分析描述 2449 panel 或已发表参考背景。查询基因型叠加会明确标为 overlay；面板统计量仍是当前计算。

    Selection scan选择扫描 unphased 167K 2449 panel only仅 2449 面板

    How to read. Screening contrast is simplified Fst (Grp vs rest) — pick a Grp. Red = sweep: that Grp’s simplified Fst (Grp vs rest) in the top 5% and within-Grp windowed heterozygosity in the bottom 5%. Blue/yellow = chromosomes. Green bands = our five named MAS/GWAS windows. The heatmap summarizes the same two statistics at those windows, followed by this sample’s overlapping sites → LocusZoom. Unphased 167K; active computation is shown below.
    怎么看：筛选对照是简化 Fst（Grp 对其余样品），请先选组。红点 = sweep：该组简化 Fst（Grp 对其余样品）最高 5% 且组内窗口杂合度最低 5%。蓝/黄=染色体。绿带=五个命名 MAS/GWAS 窗口。热图汇总这些窗口的同一套统计，随后查看本样品重合位点 → LocusZoom。未定相 167K；下方展示当前计算。
    Selection data and method. Unphased ±50 kb windowed heterozygosity + simplified Fst (Grp vs rest) on the 167K chip. LocusZoom.js 0.14.0 (Boughton et al. 2021, https://doi.org/10.1093/bioinformatics/btab186). Named MAS/GWAS windows are summarized in the active plots.
    选择数据与方法。 167K 芯片上的未定相 ±50 kb 窗口杂合度 + 简化 Fst（Grp 对其余样品）。LocusZoom.js 0.14.0（Boughton 等 2021，https://doi.org/10.1093/bioinformatics/btab186）。命名 MAS/GWAS 窗口由当前图表汇总。

    1. Genome-wide (2449 panel)1. 全基因组（2449 面板）

    Default Grp = largest n. Red = sweep. The last menu item reports Fst among all Grps. Blue/yellow identify chromosomes.
    默认 Grp = n 最大的组。红点 = sweep。最后一个菜单项报告全体 Grp 的 Fst。蓝/黄表示染色体。

    Sweep sites (this Grp)Sweep 位点（该 Grp）

    Our 167K sweep calls are shown here; literature intervals are checked separately. Red dots = this Grp’s simplified Fst (Grp vs rest) ≥ 95th and within-Grp windowed heterozygosity ≤ 5%. Sweep rows highlight the exact Manhattan site: the button pins a white star on the plot above and scrolls to it.
    这里展示 167K sweep；文献区间另行核对。红点 = 该组简化 Fst（Grp 对其余样品）≥95% 且组内窗口杂合度 ≤5%。Sweep 行会高亮精确 Manhattan 位点：按钮在上方图里钉一颗白星并滚到该图。

    5 named loci × Grp5 个命名位点 × Grp

    Why these five. These five windows are the MAS/GWAS windows on the 167K chip. (data/panel/selection_windows.tsv). Dong 2023 Table S29 intervals are checked separately in the Reference-only section, while genome-wide red sweeps use a different rule. Colour (OIV 225): classic VvMybA (2:5116947 ±10 kb) plus two Science GWAS predictors (Vvsyl02G000229, Vvsyl02G001064). Dong et al. 2023 call those two better predictors of berry skin colors than VvMybA. Flower sex (OIV 151): the SDR interval chr2:14,165,010–14,345,273. H1–H5 is Dong et al. literature context. Panel H1/H2 or other SDR tags are panel annotations. Muscat (OIV 236): VvDXS window around Science chr5:19,419,686 (panel tag 5:19418903 is 783 bp away). No OIV 241 locus overlap found in the panel GWAS. Green bands, heatmap columns, green stars, and Table A use this list.
    为什么是这五个：这五个窗口是 167K 芯片上的 MAS/GWAS 窗口。(data/panel/selection_windows.tsv)。Dong 2023 表 S29 区间在“仅作参考”部分单独核对；全基因组红色 sweep 使用另一套规则。 皮色（OIV 225）：经典 VvMybA（2:5116947 ±10 kb），加上论文里两个皮色 GWAS 预测基因 Vvsyl02G000229、Vvsyl02G001064（Dong 等 2023 写它们比 VvMybA 更能预测果皮颜色）。 花性（OIV 151）：SDR 区间 chr2:14,165,010–14,345,273。H1–H5 仅作 Dong 等文献背景。面板 H1/H2 或其他 SDR 标签是面板注释。 麝香（OIV 236）：VvDXS 窗口，论文坐标 chr5:19,419,686（芯片标签 5:19418903 相差 783 bp）。 panel GWAS 未发现 OIV 241 位点重合。绿带、热图列、绿星和 Table A 均使用这份清单。
    Columns are the five windows; rows are 2449 panel Grps. One cell = mean of chip SNPs inside that window only. The Fst cells are simplified Fst (Grp vs rest). Numbers on cells are the values; colour ranks this 12×5 table (Fst here tops out near 0.04). Click a cell → LocusZoom.
    横轴是五个窗口；纵轴是 2449 面板 Grp。一格 = 该窗口内芯片位点的平均。Fst 格是简化 Fst（Grp 对其余样品）。格子上的数字才是数值，颜色表示这张 12×5 表的相对深浅（这里 Fst 最高约 0.04）。点一格跳 LocusZoom。

    Fst vs hetFst 与杂合度

    Grey is the shared deterministic stride-30 subsample; green stars are means of all SNPs in the named windows — the same mean het / Fst among all Grps as Table A. The y-axis is Fst among all Grps. The SDR window stays heterozygous in the panel; H1–H5 remains Dong et al. literature context, and panel SDR tags are panel annotations.
    灰点是共用确定性 stride-30 子样本；绿星是命名窗口内所有 SNP 的均值，与表 A 的 mean het / 全体 Grp 的 Fst 相同。纵轴是全体 Grp 的 Fst。SDR 窗口在 panel 中仍保持杂合；H1–H5 仅作 Dong 等文献背景，面板 SDR 标签是面板注释。

    2. This sample at overlapping sites2. 本样品重合位点

    3. Panel regional context (among-Grps Fst)3. 面板区域背景（全体 Grp 的 Fst）

    Panel regional context (among-Grps Fst). LocusZoom covers the five named windows, S29 windows with chip coverage, and overall among-Grps peaks already present in selection_loci. This view reports regional panel context; the active sweep contrast is shown above.
    面板区域背景（全体 Grp 的 Fst）。 LocusZoom 覆盖五个命名窗口、有芯片覆盖的 S29 窗口，以及 selection_loci 中已有的全体 Grp 峰。这里报告面板区域背景；上方展示当前 sweep 对照。
    Reference only.仅作核对。 Reference only仅作核对 Reference-only S29 overlap check. Dong 2023 shared CG1∩CG2 domestication bins (paper Table S29) — reference context.仅作参考的 S29 重合核对。Dong 2023 CG1∩CG2 共同驯化区间（论文表 S29）— 文献背景。
    Dong et al. 2023 Science 379:892–901, doi:10.1126/science.add8655. They scanned Syl-E1/CG1 and Syl-E2/CG2 against their wild pairs; the main-text rule used increased nucleotide-diversity difference and population differentiation, both top 5% (Fig. 3D). Table S28 contains the two group lists; Table S29 is the intersection of the two lists: 189 genes in 31 regions. This section reports the 167K chip interval-overlap check and the overlap with our five MAS/GWAS windows. Our extract has 30 unique intervals (paper: 31 regions).
    Dong 等 2023《Science》379:892–901，doi:10.1126/science.add8655。论文比较 Syl-E1/CG1 和 Syl-E2/CG2 与野生配对组，正文规则要求核苷酸多样性差异和群体分化均进入前 5%（图 3D）。表 S28 是两组清单；表 S29 是两组清单的交集，含 189 个基因、31 个区间。本节报告 167K 芯片区间重合，以及与五个 MAS/GWAS 窗口的重合。我们的提取有 30 个不重复区间（论文为 31 个）。

    Trait loci性状位点 2449 panel only仅 2449 面板

    How to read. Design-time overlap of this 167K panel with GWAS/MAS trait loci. IDs in the table are outbound database links. Gene product/GO are SwissProt BLAST xrefs (homology).
    怎么看：167K panel 与 GWAS/MAS 性状位点的设计期重叠。表中 ID 是外链。产物/GO 是 SwissProt BLAST 同源注释。
    Panel overlap with design-time GWAS/MAS loci (up to 40 rows, round-robin across traits; Dong 2023 MAS colour/SDR sites first). Gene span / strand / region from the VS-1 annotation. OIV descriptors from the OIV 2009 list. OIV codes link to EU-Vitis descriptor PDFs (http://www.eu-vitis.de/docs/descriptors/oivdesc/) and the OIV 2009 2nd edition list (https://www.oiv.int/node/2830). Some des-cep-only codes have no PDF. Product / GO / Pfam / InterPro / EC are SwissProt BLAST xrefs (DIAMOND bits ≥ 100; UniProt REST of the hit accession — homology). Grape IDs: Ensembl Plants PN40024.T2T ASM3070453v1 pep (gene / gene_symbol), Entrez / RefSeq TSV, KEGG vvi via NCBI GeneID. Buchfink et al. 2021 Nat Methods 18:366, https://doi.org/10.1038/s41592-021-01101-x; UniProt API https://www.uniprot.org/help/api_queries ; Ensembl Plants https://plants.ensembl.org/Vitis_vinifera/Info/Index ; KEGG REST https://www.kegg.jp/kegg/rest/keggapi.html ; NCBI gene_info https://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Plants/ . IDs in the table are outbound record links (QuickGO, InterPro/Pfam, KEGG, Ensembl Plants, NCBI Gene, UniProt, Expasy EC, OIV). Known aliases from Dong et al. 2023 Science 379:892–901 (doi:10.1126/science.add8655).
    面板与设计期 GWAS/MAS 位点的重合 （最多 40 行，按性状轮转；Dong 2023 的皮色/SDR 位点优先）。 基因跨度 / 链 / 区域来自 VS-1 注释。 OIV 描述符来自 OIV 2009 清单。 OIV 代码链到 EU-Vitis 描述符 PDF （http://www.eu-vitis.de/docs/descriptors/oivdesc/）和 OIV 2009 第 2 版清单 （https://www.oiv.int/node/2830）。部分仅 des-cep 代码没有 PDF。 产物 / GO / Pfam / InterPro / EC 是 SwissProt BLAST 交叉引用 （DIAMOND bits ≥ 100；命中登录号的 UniProt REST — 同源）。 葡萄 ID：Ensembl Plants PN40024.T2T ASM3070453v1 pep（gene / gene_symbol）、 Entrez / RefSeq TSV、经 NCBI GeneID 的 KEGG vvi。 Buchfink 等 2021 Nat Methods 18:366，https://doi.org/10.1038/s41592-021-01101-x； UniProt API https://www.uniprot.org/help/api_queries ； Ensembl Plants https://plants.ensembl.org/Vitis_vinifera/Info/Index ； KEGG REST https://www.kegg.jp/kegg/rest/keggapi.html ； NCBI gene_info https://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Plants/ 。 表中 ID 是外链记录（QuickGO、InterPro/Pfam、KEGG、Ensembl Plants、NCBI Gene、UniProt、Expasy EC、OIV）。 已知别名来自 Dong 等 2023 Science 379:892–901 （doi:10.1126/science.add8655）。

    Panel GWAS / panel GS面板育种 2449 panel only仅 2449 面板

    How to read. Panel GWAS/GS index. LocusZoom: drag to pan, scroll to zoom, click a SNP or gene. Association / r² / β are panel EMMAX/P3D. The panel track supplies the query genotype overlay; per-query GS predictions are reported above.
    怎么看：panel 的 GWAS/GS 索引。LocusZoom 可拖动平移、滚轮缩放、点击 SNP 或基因。关联/r²/β 来自 2449；panel 轨道提供查询样本基因型叠加；逐样本 GS 预测见上方。
    GWAS / GS panel index and regional context. Regional plot is LocusZoom.js 0.14.0 (Boughton et al. 2021, https://doi.org/10.1093/bioinformatics/btab186; classic layout Pruim et al. 2010, https://doi.org/10.1093/bioinformatics/btq419). Association points and gene track are the library. LD colour = panel-dosage r² to the lead (2449 freeze). Genes = VS-1 GFF. Query GT is this sample. Panel GWAS sites: 13,950 design-time loci; n≈400. Binary case/control counts come from each trait’s summary.json; imbalanced binary traits need caution. See docs/METHODS_breeding.md and Kang et al. 2010 EMMAX/LMM (https://doi.org/10.1038/ng.548).
    GWAS / GS 面板索引与区域背景。 区域图是 LocusZoom.js 0.14.0 （Boughton 等 2021，https://doi.org/10.1093/bioinformatics/btab186； 经典布局 Pruim 等 2010，https://doi.org/10.1093/bioinformatics/btq419）。 关联点和基因轨道来自该库。 LD 颜色 = 相对主位点的面板 dosage r²（2449 冻结）。 基因 = VS-1 GFF。Query GT 是本样品。 面板 GWAS 位点：13,950 个设计期位点；n≈400。 二元病例/对照计数来自各性状的 summary.json；不平衡二元性状需谨慎。 见 docs/METHODS_breeding.md 与 Kang 等 2010 EMMAX/LMM （https://doi.org/10.1038/ng.548）。

    LocusZoom (panel GWAS)LocusZoom（面板 GWAS）

    Official LocusZoom.js: drag to pan, scroll to zoom, click a SNP or gene. Association / r² / β = panel EMMAX/P3D. Genes = VS-1. Query GT = this sample. Boughton et al. 2021, https://doi.org/10.1093/bioinformatics/btab186.
    官方 LocusZoom.js：拖动平移、滚轮缩放、点击 SNP 或基因。关联/r²/β = panel EMMAX/P3D；基因 = VS-1；Query GT = 本样品分型。Boughton 等 2021，https://doi.org/10.1093/bioinformatics/btab186。

    GS accuracyGS 准确度

    Top crosses推荐杂交组合

    Methods方法说明

    How to read. Appendix: PCA method, 4K identity cutoffs, ADMIXTURE K=2–8 colours, QC rate definitions, and selection/f3 caveats. Read this last; the plots above are the working view.
    怎么看：附录。PCA 方法、4K 身份阈值、ADMIXTURE 着色、QC 定义、选择/f3 限制。工作浏览请看上面各节，方法放最后。
    PCA method: Loading…. PC1–PC3 are displayed when available; reported percentages use explained-variance fractions only.
    PCA 方法：加载中…。 有 PC1–PC3 时显示；报告百分比只用解释方差分数。
    Identity (4K): Identical R1≥1.2 + IBS2*%≥0.99 + KING≥0.3426; PO: 0.5<R1<1.2 + 0.21≤KING<0.3426 + R0≤0.096. Full sib 0.177≤KING<0.354; 2nd 0.0884≤KING<0.177; 3rd 0.0442≤KING<0.0884. KING estimator: Manichaikul et al. 2010, doi:10.1093/bioinformatics/btq559. Self-in-panel reported as QC then nearest non-self.
    身份（4K）：完全相同 R1≥1.2 + IBS2*%≥0.99 + KING≥0.3426； 亲子：0.5<R1<1.2 + 0.21≤KING<0.3426 + R0≤0.096。全同胞 0.177≤KING<0.354；二级 0.0884≤KING<0.177；三级 0.0442≤KING<0.0884。KING 估计见 Manichaikul 等 2010，doi:10.1093/bioinformatics/btq559。面板内自身先作质控，再报告最近非自身。
    Other kinship rules (same pairs, different gates; the clone section can switch them when IBS0 and P0 were stored). Ramos-Madrigal et al. 2019, doi:10.1038/s41477-019-0437-5: identical clone KING≥0.49 and IBS0≤0.001; parent–offspring 0.177<KING<0.354 and IBS0≤0.001; the same KING window with IBS0>0.001 is labeled highly related. READv2, Alaçamlı et al. 2024, doi:10.1186/s13059-024-03350-3: normalized P0 cutoffs 0.625 / 0.8125 / 0.90625 / 0.953125 (READ2.py v2.01). First degree is not split further on this SNP panel.
    其他亲缘规则（同一批配对，不同的门；克隆板块在存有 IBS0 和 P0 时可以切换）。 Ramos-Madrigal 等 2019，doi:10.1038/s41477-019-0437-5：克隆 KING≥0.49 且 IBS0≤0.001；亲子 0.177<KING<0.354 且 IBS0≤0.001；同一 KING 窗口里 IBS0>0.001 标为高度相关。 READv2，Alaçamlı 等 2024，doi:10.1186/s13059-024-03350-3：标准化 P0 阈值 0.625 / 0.8125 / 0.90625 / 0.953125（READ2.py v2.01）。在这套 SNP 上不再把一级亲缘拆开。
    ADMIXTURE: Loading…
    ADMIXTURE：加载中…
    Source:
    来源：
    Loading…加载中…
    QC calling rates: panel rate = called / 167K panel sites (primary); VCF-site rate = called / sites present in the sample VCF.
    QC 分型率：panel 分型率 = 已分型 / 167K 面板位点（主指标）； VCF-site 分型率 = 已分型 / 本样品 VCF 中的位点。
    Scope boundary: exclusions and literature comparisons are summarized here. Reader-facing panels above lead with their active computation. Selection: unphased ±50 kb windowed heterozygosity + simplified Fst (Grp vs rest) on the 167K chip; sweep = Fst ≥95th ∩ within-Grp windowed heterozygosity ≤5th. Regional / Table A context uses Fst among all Grps. These Fst values are a simplified estimator, not a canonical Weir–Cockerham implementation. Dong 2023 Table S29 (doi:10.1126/science.add8655) is the CG1∩CG2 shared-bin reference (189 genes / 31 regions), and its interval overlap is reported separately. Regional view is LocusZoom.js (Y = Fst among all Grps or windowed heterozygosity). Displayed PCA uses frozen GCTA64 GRM-PCA axes with least-squares query projection, not a 5k-SNP SVD. f3/f4 are exploratory 2449 panel Grp-mean allele-frequency summaries with complete-case n_sites and n_blocks (Patterson et al. 2012, doi:10.1534/genetics.112.145037).
    范围边界：排除项和文献比较统一在这里说明。 上方读者区域优先展示当前计算。选择扫描使用 167K 未定相窗口杂合度与简化 Fst（Grp 对其余样品）；sweep 使用 Fst ≥95% 且组内窗口杂合度 ≤5%。区域 / 表 A 使用全体 Grp 的 Fst。这些 Fst 是简化估计，不是规范 Weir–Cockerham 实现。Dong 2023 表 S29（doi:10.1126/science.add8655）是 CG1∩CG2 共同区间参考（189 个基因 / 31 个区间），其区间重合单独报告。区域图使用 LocusZoom.js；显示的 PCA 使用冻结 GCTA64 GRM-PCA 轴加最小二乘查询投影，不是 5k SNP 的 SVD。f3/f4 是探索性的 2449 面板 Grp 均值等位基因频率汇总，并报告完整案例 n_sites 和 n_blocks（Patterson 等 2012，doi:10.1534/genetics.112.145037）。

    Downloads下载

    How to use. This query’s own tables only (QC, this sample’s Q, damage, clone/PO, kinship). The 2449 reference is not included. Missing query sidecars do not indicate analysis failure.怎么用：只下载本检测样本的结果。2449 参考库不提供下载。查询 sidecar 缺失不表示分析失败。