1 Methods

For each compartment file and chromosome, protein-coding gene spans were counted per AB bin using interval overlap. The gene-span signal was correlated with raw E1 using Spearman correlation. A negative raw correlation indicates a chromosome that needed sign flipping during phasing. The significance values below are Spearman cor.test p-values, with BH FDR correction across all chromosome-by-file tests.

The plotted phased_rho is sign-adjusted after phasing: raw positive rho is kept, and raw negative rho is multiplied by -1.

2 Overall Summary

Genome Sample Chromosomes Flipped FDR < 0.05 Min phased rho Median phased rho Max FDR
Eluc - Northern pike L11 25 1 25 0.498 0.603 2.51e-36
Eluc - Northern pike brain 25 0 25 0.533 0.641 3.21e-40
Eluc - Northern pike gill 25 2 25 0.535 0.618 3.45e-40
Omyk - Rainbow trout brain 32 13 29 0.014 0.334 6.18e-01
Omyk - Rainbow trout gill 32 15 32 0.089 0.507 1.41e-03
Omyk - Rainbow trout liver 32 15 32 0.223 0.465 1.79e-15
Salp - Arctic char B34 39 19 37 0.013 0.369 6.77e-01
Salp - Arctic char gill 39 20 39 0.168 0.521 7.43e-06
Salp - Arctic char liver 39 22 39 0.214 0.453 7.05e-09
Ssal - Atlantic salmon B35 29 13 29 0.224 0.461 1.89e-21
Ssal - Atlantic salmon gill 29 11 29 0.228 0.538 4.63e-20
Ssal - Atlantic salmon liver 29 15 29 0.131 0.452 1.47e-07
Tthy - Grayling brain 50 30 50 0.265 0.502 7.64e-08
Tthy - Grayling liver 50 28 50 0.090 0.510 4.06e-02
Upyg - Eastern mudminnow B30 11 0 11 0.415 0.539 1.37e-154
Upyg - Eastern mudminnow gill 11 0 11 0.510 0.596 4.67e-215
Upyg - Eastern mudminnow liver 11 1 11 0.357 0.467 5.75e-91

The per-chromosome statistics table was written to:

/Users/larsgronvold/Downloads/ThreeD/reports/phasing_quality/phasing_quality_by_chromosome.tsv

3 Genome-Level Plots

3.1 Eluc - Northern pike

Sample File Chromosomes Flipped FDR < 0.05 Min phased rho Median phased rho Max FDR
L11 ab_compartment_L11_El.tsv 25 1 25 0.498 0.603 2.51e-36
brain ab_compartment_brain_El.tsv 25 0 25 0.533 0.641 3.21e-40
gill ab_compartment_gill_El.tsv 25 2 25 0.535 0.618 3.45e-40

3.2 Omyk - Rainbow trout

Sample File Chromosomes Flipped FDR < 0.05 Min phased rho Median phased rho Max FDR
brain ab_compartment_brain_Om.tsv 32 13 29 0.014 0.334 6.18e-01
gill ab_compartment_gill_Om.tsv 32 15 32 0.089 0.507 1.41e-03
liver ab_compartment_liver_Om.tsv 32 15 32 0.223 0.465 1.79e-15

3.3 Salp - Arctic char

Sample File Chromosomes Flipped FDR < 0.05 Min phased rho Median phased rho Max FDR
B34 ab_compartment_B34_Sa.tsv 39 19 37 0.013 0.369 6.77e-01
gill ab_compartment_gill_Sa.tsv 39 20 39 0.168 0.521 7.43e-06
liver ab_compartment_liver_Sa.tsv 39 22 39 0.214 0.453 7.05e-09

3.4 Ssal - Atlantic salmon

Sample File Chromosomes Flipped FDR < 0.05 Min phased rho Median phased rho Max FDR
B35 ab_compartment_B35_Ss.tsv 29 13 29 0.224 0.461 1.89e-21
gill ab_compartment_gill_Ss.tsv 29 11 29 0.228 0.538 4.63e-20
liver ab_compartment_liver_Ss.tsv 29 15 29 0.131 0.452 1.47e-07

3.5 Tthy - Grayling

Sample File Chromosomes Flipped FDR < 0.05 Min phased rho Median phased rho Max FDR
brain ab_compartment_brain_Tt.tsv 50 30 50 0.265 0.502 7.64e-08
liver ab_compartment_liver_Tt.tsv 50 28 50 0.090 0.510 4.06e-02

3.6 Upyg - Eastern mudminnow

Sample File Chromosomes Flipped FDR < 0.05 Min phased rho Median phased rho Max FDR
B30 ab_compartment_B30_Up.tsv 11 0 11 0.415 0.539 1.37e-154
gill ab_compartment_gill_Up.tsv 11 0 11 0.510 0.596 4.67e-215
liver ab_compartment_liver_Up.tsv 11 1 11 0.357 0.467 5.75e-91

4 Significance Legend

The report uses BH-adjusted FDR across all chromosome-by-file tests:

The heatmap fill uses -log10(FDR), capped at 50 so that extremely small p-values do not flatten the color scale.