QC-Report

Allele-Frequency Correlation

Uploaded Samples vs. Reference Panel

The plot shows the densities of frequencies falling into each part (excluding chromosome X). The first 5000 points from areas of lowest regional densities will be plotted.

Potential Frequency Mismatches

Markers where chisq is greater than 300.

## Total mismatches: 15Mismatched frequencies for '10:111850503' f[A,G] = [0.1301775,0.8698225] vs [0.5358,0.4642], chisq 437.1397
## Mismatched frequencies for '11:14181174' f[T,C] = [0.5716332,0.4283668] vs [0.8344,0.1656], chisq 332.6191
## Mismatched frequencies for '11:114432867' f[G,A] = [0.8627167,0.1372832] vs [0.5251,0.4749], chisq 310.209
## Mismatched frequencies for '11:119648458' f[A,C] = [0.1331361,0.8668639] vs [0.5391,0.4609], chisq 438.2137
## Mismatched frequencies for '15:78269472' f[A,G] = [0.04782608,0.9521739] vs [0.8095,0.1905], chisq 2393.442
## Mismatched frequencies for '16:9397933' f[G,A] = [0.9186047,0.08139535] vs [0.5823,0.4177], chisq 314.8328
## Mismatched frequencies for '16:71029103' f[C,T] = [0.9020468,0.09795321] vs [0.9963,0.0037], chisq 1060.29
## Mismatched frequencies for '18:72083984' f[G,T] = [0.7926471,0.2073529] vs [0.9997,3e-04], chisq 6308.149
## Mismatched frequencies for '19:55357424' f[T,C] = [0.3836207,0.6163793] vs [0.8917,0.1083], chisq 1678.255
## Mismatched frequencies for '1:65872597' f[A,C] = [0.1079882,0.8920118] vs [0.5151,0.4849], chisq 439.1022
## Mismatched frequencies for '4:75479060' f[G,A] = [0.2627841,0.7372159] vs [0.9851,0.0149], chisq 12263.78
## Mismatched frequencies for '5:166465008' f[A,G] = [0.1011396,0.8988604] vs [0.444,0.556], chisq 328.3595
## Mismatched frequencies for '5:170961300' f[C,T] = [0.1181556,0.8818444] vs [0.4726,0.5274], chisq 343.1168
## Mismatched frequencies for '8:1154309' f[T,G] = [0.1316568,0.8683432] vs [0.5278,0.4722], chisq 416.3306
## Mismatched frequencies for '8:33679271' f[G,A] = [0.9730539,0.02694611] vs [0.9993,7e-04], chisq 367.2983