普通牛填充面板准确性测试
Note
填充面板信息
72个品种，每个品种45个样本
测试样本信息
每个品种5个左右，分别downsample到1x，0.5x，0.1x之后，GLIMPE2进行填充
准确性评估
位点平均准确性
1x
输入文件: chr1_bam_lst.new.error.grp.txt.gz
标签: chr1
MAF bins: [0.0, 0.001, 0.002, 0.005, 0.01, 0.05, 0.1, 0.2, 0.5]
输出图片: chr1.accuracy.grp.png
输出统计: chr1.accuracy.grp.stats
正在解析 chr1_bam_lst.new.error.grp.txt.gz...
✓ 成功解析 8 个 MAF bins
Concordance: 0.975 - 0.999
r² (GT): 0.814 - 0.952
r² (DS): 0.837 - 0.962
MAF bins信息:
Bin 0: [0.00000,0.00100), center: 0.00050
Bin 1: [0.00100,0.00200), center: 0.00150
Bin 2: [0.00200,0.00500), center: 0.00350
Bin 3: [0.00500,0.01000), center: 0.00750
Bin 4: [0.01000,0.05000), center: 0.03000
Bin 5: [0.05000,0.10000), center: 0.07500
Bin 6: [0.10000,0.20000), center: 0.15000
Bin 7: [0.20000,0.50000), center: 0.35000
✓ 统计数据已保存: chr1.accuracy.grp.stats
✓ 图片已保存: chr1.accuracy.grp.png
=== 统计摘要 ===
平均 Concordance: 0.9923
平均 r² (GT): 0.9065
平均 r² (DS): 0.9204
MAF_bin Concordance r2_GT r2_DS
[0.00000,0.00100) 0.998525 0.813665 0.836579
[0.00100,0.00200) 0.999286 0.852691 0.872747
[0.00200,0.00500) 0.999037 0.896606 0.910907
[0.00500,0.01000) 0.998579 0.921185 0.932606
[0.01000,0.05000) 0.996553 0.936330 0.946577
[0.05000,0.10000) 0.989590 0.938531 0.949544
[0.10000,0.20000) 0.981511 0.941459 0.952381
[0.20000,0.50000) 0.975109 0.951854 0.961579
0.5x
输入文件: chr1.05_bam_lst.error.grp.txt.gz
标签: chr1.05
MAF bins: [0.0, 0.001, 0.002, 0.005, 0.01, 0.05, 0.1, 0.2, 0.5]
输出图片: chr1.05.accuracy.grp.png
输出统计: chr1.05.accuracy.grp.stats
正在解析 chr1.05_bam_lst.error.grp.txt.gz...
✓ 成功解析 8 个 MAF bins
Concordance: 0.968 - 0.999
r² (GT): 0.789 - 0.939
r² (DS): 0.817 - 0.952
MAF bins信息:
Bin 0: [0.00000,0.00100), center: 0.00050
Bin 1: [0.00100,0.00200), center: 0.00150
Bin 2: [0.00200,0.00500), center: 0.00350
Bin 3: [0.00500,0.01000), center: 0.00750
Bin 4: [0.01000,0.05000), center: 0.03000
Bin 5: [0.05000,0.10000), center: 0.07500
Bin 6: [0.10000,0.20000), center: 0.15000
Bin 7: [0.20000,0.50000), center: 0.35000
✓ 统计数据已保存: chr1.05.accuracy.grp.stats
✓ 图片已保存: chr1.05.accuracy.grp.png
=== 统计摘要 ===
平均 Concordance: 0.9903
平均 r² (GT): 0.8892
平均 r² (DS): 0.9067
0.1x
标签: chr1.01x 16:03:57 [20/9979]
MAF bins: [0.0, 0.001, 0.002, 0.005, 0.01, 0.05, 0.1, 0.2, 0.5]
输出图片: chr1.01x_imputation_accuracy.grp.png
输出统计: chr1.01x.accuracy.grp.stats
正在解析 chr1.01x_bam_lst.error.grp.txt.gz...
✓ 成功解析 8 个 MAF bins
Concordance: 0.935 - 0.999
r² (GT): 0.702 - 0.881
r² (DS): 0.745 - 0.907
MAF bins信息:
Bin 0: [0.00000,0.00100), center: 0.00050
Bin 1: [0.00100,0.00200), center: 0.00150
Bin 2: [0.00200,0.00500), center: 0.00350
Bin 3: [0.00500,0.01000), center: 0.00750
Bin 4: [0.01000,0.05000), center: 0.03000
Bin 5: [0.05000,0.10000), center: 0.07500
Bin 6: [0.10000,0.20000), center: 0.15000
Bin 7: [0.20000,0.50000), center: 0.35000
✓ 统计数据已保存: chr1.01x.accuracy.grp.stats
✓ 图片已保存: chr1.01x_imputation_accuracy.grp.png
=== 统计摘要 ===
平均 Concordance: 0.9808
平均 r² (GT): 0.8197
平均 r² (DS): 0.8504
MAF_bin Concordance r2_GT r2_DS
[0.00000,0.00100) 0.997647 0.701640 0.744573
[0.00100,0.00200) 0.998858 0.766466 0.798443
[0.00200,0.00500) 0.998176 0.806488 0.837080
[0.00500,0.01000) 0.996937 0.833114 0.861321
[0.01000,0.05000) 0.992064 0.856455 0.883387
[0.05000,0.10000) 0.974693 0.855111 0.884565
[0.10000,0.20000) 0.952899 0.857114 0.887021
[0.20000,0.50000) 0.935364 0.881087 0.907114
不同样本的平均准确性
1x
输入文件: chr1_bam_lst.new.error.spl.txt.gz
标签: chr1
输出图片: chr1.accuracy.spl.png
输出统计: chr1.accuracy.spl.stats
正在解析 chr1_bam_lst.new.error.spl.txt.gz...
✓ 成功解析 38 个样本
Concordance: 0.9887 - 0.9965
r² (GT): 0.9481 - 0.9742
r² (DS): 0.9581 - 0.9785
✓ 统计数据已保存: chr1.accuracy.spl.stats
✓ 图片已保存: chr1.accuracy.spl.png
=== 统计摘要 ===
样本数量: 38
平均 Concordance: 0.9924 ± 0.0023
平均 r² (GT): 0.9623 ± 0.0065
平均 r² (DS): 0.9694 ± 0.0052
最佳样本: 0202501
Concordance: 0.9962
r² (DS): 0.9785
最差样本: 0201972
Concordance: 0.9892
r² (DS): 0.9581
Sample Concordance r2_GT r2_DS
0202002 0.990546 0.956671 0.965076
0201870 0.991606 0.963510 0.970468
0202401 0.994032 0.967116 0.973557
0201973 0.990382 0.957304 0.965556
0201863 0.992192 0.965614 0.972563
0202205 0.991248 0.966702 0.973118
0202403 0.993628 0.966043 0.972250
0202005 0.992087 0.960517 0.968069
0202404 0.993429 0.961684 0.968987
0202504 0.993838 0.958923 0.966858
0202503 0.995523 0.968411 0.974489
0201880 0.988743 0.951726 0.960579
0202203 0.990995 0.968297 0.974513
0202806 0.991054 0.965974 0.972532
0201873 0.991550 0.961531 0.969205
0202003 0.990431 0.949026 0.958498
0202801 0.989206 0.962362 0.969427
0202952 0.996490 0.971943 0.976683
0202954 0.996386 0.970835 0.976524
0202803 0.990789 0.963889 0.970599
0202951 0.995682 0.966060 0.972281
0202805 0.990692 0.963657 0.970307
0201975 0.990717 0.954878 0.963160
0202201 0.991019 0.966498 0.972843
0202955 0.996384 0.968374 0.973789
0202004 0.992113 0.955121 0.963407
0201874 0.991402 0.960983 0.968410
0202202 0.990479 0.964702 0.971520
0202501 0.996194 0.974187 0.978479
0201978 0.989803 0.953252 0.962204
0201971 0.991164 0.957154 0.965405
0202001 0.991656 0.952241 0.961287
0202804 0.989905 0.965732 0.972413
0201972 0.989156 0.948086 0.958122
0202405 0.992385 0.965205 0.971740
0202505 0.994657 0.959091 0.967151
0202953 0.996497 0.973006 0.977978
0202502 0.995310 0.961543 0.968715
0.5x
标签: chr1.05
输出图片: chr1.05.accuracy.spl.png
输出统计: chr1.05.accuracy.spl.stats
正在解析 chr1.05_bam_lst.error.spl.txt.gz...
✓ 成功解析 38 个样本
Concordance: 0.9858 - 0.9956
r² (GT): 0.9375 - 0.9694
r² (DS): 0.9498 - 0.9751
✓ 统计数据已保存: chr1.05.accuracy.spl.stats
✓ 图片已保存: chr1.05.accuracy.spl.png
=== 统计摘要 ===
样本数量: 38
平均 Concordance: 0.9903 ± 0.0030
平均 r² (GT): 0.9528 ± 0.0077
平均 r² (DS): 0.9623 ± 0.0061
最佳样本: 0202501
Concordance: 0.9955
r² (DS): 0.9751
最差样本: 0201972
Concordance: 0.9869
r² (DS): 0.9498
Sample Concordance r2_GT r2_DS
0202955 0.995525 0.961082 0.968317
0202954 0.995489 0.963596 0.971421
0202952 0.995570 0.964701 0.971325
0202951 0.994506 0.956955 0.965943
0202805 0.987801 0.952632 0.961775
0202804 0.987277 0.956965 0.965735
0202803 0.988358 0.954565 0.964164
0202001 0.989751 0.941668 0.953283
0201973 0.988162 0.947803 0.958337
0201971 0.988972 0.946778 0.957962
0201978 0.987101 0.941210 0.952938
0201975 0.987974 0.941894 0.954265
0202201 0.988400 0.956954 0.965380
0202002 0.988642 0.948159 0.958607
0201972 0.986896 0.937539 0.949759
0202405 0.990559 0.957052 0.965594
0201880 0.985807 0.939683 0.951063
0202202 0.988260 0.956670 0.965321
0202003 0.988190 0.937499 0.950848
0201873 0.988965 0.950169 0.960431
0202005 0.989974 0.950334 0.961023
0201870 0.989136 0.953083 0.962567
0201863 0.989718 0.955001 0.964422
0201874 0.989181 0.951251 0.960724
0202004 0.990731 0.947449 0.957655
0202806 0.988241 0.955518 0.964825
0202203 0.987983 0.957932 0.966635
0202205 0.988263 0.955538 0.965200
0202953 0.995579 0.966033 0.973126
0202502 0.994080 0.951665 0.960752
0202401 0.992132 0.956909 0.965882
0202403 0.992250 0.958759 0.966928
0202801 0.985884 0.951079 0.961106
0202404 0.991514 0.950867 0.960590
0202504 0.992419 0.949747 0.959556
0202501 0.995481 0.969359 0.975130
0202503 0.994424 0.960904 0.968390
0202505 0.993586 0.950950 0.960483
0.1x
输入文件: chr1.01x_bam_lst.error.spl.txt.gz
标签: chr1.01x
输出图片: chr1.01x.accuracy.spl.png
输出统计: chr1.01x.accuracy.spl.stats
正在解析 chr1.01x_bam_lst.error.spl.txt.gz...
✓ 成功解析 38 个样本
Concordance: 0.9727 - 0.9925
r² (GT): 0.8793 - 0.9494
r² (DS): 0.9045 - 0.9605
✓ 统计数据已保存: chr1.01x.accuracy.spl.stats
✓ 图片已保存: chr1.01x.accuracy.spl.png
=== 统计摘要 ===
样本数量: 38
平均 Concordance: 0.9810 ± 0.0067
平均 r² (GT): 0.9101 ± 0.0165
平均 r² (DS): 0.9297 ± 0.0131
最佳样本: 0202501
Concordance: 0.9925
r² (DS): 0.9605
最差样本: 0201972
Concordance: 0.9739
r² (DS): 0.9045
Sample Concordance r2_GT r2_DS
0202955 0.991395 0.925637 0.940872
0202954 0.992052 0.936988 0.951197
0202952 0.991388 0.932290 0.946683
0202951 0.988295 0.910279 0.929537
0202805 0.973219 0.898666 0.920254
0202804 0.974172 0.914381 0.933605
0202803 0.974594 0.903861 0.923742
0202001 0.981602 0.897229 0.919701
0201973 0.975368 0.893812 0.916892
0201971 0.975886 0.888597 0.911689
0201978 0.972770 0.879819 0.906191
0201975 0.975369 0.884026 0.909729
0202201 0.973419 0.903292 0.923626
0202002 0.978193 0.903283 0.924944
0201972 0.973948 0.879309 0.904514
0202405 0.982371 0.921158 0.939005
0201880 0.973493 0.890439 0.914315
0202202 0.976703 0.915362 0.933133
0202003 0.979615 0.894418 0.917042
0201873 0.979243 0.908190 0.928778
0202005 0.982300 0.914104 0.932352
0201870 0.979579 0.913604 0.932243
0201863 0.980345 0.915433 0.934768
0201874 0.977649 0.901241 0.922531
0202004 0.981548 0.897822 0.920842
0202806 0.975538 0.909618 0.930048
0202203 0.974307 0.911735 0.931437
0202205 0.974766 0.906561 0.928139
0202953 0.991223 0.933575 0.948004
0202502 0.987092 0.896309 0.918630
0202401 0.985147 0.919900 0.937406
0202403 0.987461 0.934425 0.950321
0202801 0.972653 0.907065 0.926790
0202404 0.987265 0.926488 0.942420
0202504 0.987576 0.919006 0.936712
0202501 0.992501 0.949361 0.960479
0202503 0.990155 0.931444 0.947585
0202505 0.988435 0.913617 0.932714