Summary

Basic Descriptive Statistics
! Data Leakage
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Automated quality control for genomic machine learning datasets: scores the biases, duplicates and data leakage a classifier could exploit before you train on it.
Searching test set human_enhancers_cohn_test.csv.gz against train set human_enhancers_cohn_train.csv.gz
Data Leakage:!WarningHow a flag is decided →
gb-qc v1.0.0 · run 2026-09-15 22:31:05

Basic Descriptive Statistics

Filename human_enhancers_cohn_test.csv.gz human_enhancers_cohn_train.csv.gz
Number of sequences 6948 20843
Minimum length 500 500
Mean length 500.00 500.00
Maximum length 500 500
!

Data Leakage

Every test sequence searched against the train set with MMseqs2, and scored on its best hit. Similarity is min(query coverage, target coverage) × percent identity: how much of the shorter sequence the alignment spans, times how much of that matches. The histogram is the distribution of those best hits.

The flag is the percentage of test sequences at or above the threshold: Pass at 0%, Warning below 2%, Fail at 2% or more. A test sequence that near-duplicates a training one is one the model has already seen, so the accuracy it earns there is not evidence. What to do about it →

The panel under the histogram lists those alignments, up to the first 100; every one of them, listed or not, is exported to mmseqs/mmseqs2_search_result.tsv beside this report. Its columns are:

Query (Q)
Identifier of the test sequence: seq_<i>_test, where i is its 0-based position in the input test file.
Target (T)
Identifier of the train sequence: seq_<i>_train, where i is its 0-based position in the input train file.
Q Cov.
Fraction of the query sequence covered by the alignment (0–1).
T Cov.
Fraction of the target sequence covered by the alignment (0–1).
% Identity
Percent identical aligned positions in the aligned region.
% Similarity
Similarity score used for leakage detection, calculated as min(Q Cov., T Cov.) × % Identity.
E-value
MMseqs2 E-value (lower is more "significant").
Alignment
Click “Show” to expand the alignment visualisation for a row.
Filename human_enhancers_cohn_test.csv.gz human_enhancers_cohn_train.csv.gz
Data Leakage (percentage) 0.85% 0.38%
Data Leakage (count) 59 80
Similarity Histogram
93 high-similarity alignments
Query (Q) Target (T) Q Cov. T Cov. % Identity % Similarity E-value Alignment
seq_4977_test seq_16656_train 1.00 1.00 99.7 99.50 5.25e-275
seq_1480_test seq_1359_train 0.99 0.99 100.0 99.20 1.14e-274
seq_1392_test seq_3374_train 0.99 0.99 100.0 99.20 1.14e-274
seq_2130_test seq_8630_train 1.00 1.00 96.9 96.71 9.75e-252
seq_3291_test seq_6337_train 1.00 0.99 96.9 96.32 9.05e-250
seq_722_test seq_4993_train 1.00 1.00 95.5 95.31 2.51e-240
seq_882_test seq_844_train 0.98 0.97 97.1 94.58 7.16e-245
seq_3004_test seq_61_train 0.99 0.99 95.7 94.36 4.59e-238
seq_3194_test seq_6467_train 0.98 0.98 96.5 94.18 2.68e-241
seq_137_test seq_1236_train 0.99 0.99 95.3 94.16 7.61e-235
seq_304_test seq_5861_train 0.99 0.99 94.7 94.13 2.31e-230
seq_1655_test seq_340_train 0.99 1.00 94.5 93.93 4.82e-230
seq_664_test seq_8417_train 0.97 0.97 96.5 93.80 5.29e-240
seq_3194_test seq_4053_train 0.99 0.98 95.3 93.78 1.73e-235
seq_832_test seq_3430_train 0.99 1.00 94.9 93.76 1.59e-234
seq_2443_test seq_3627_train 0.99 0.99 94.5 93.55 4.36e-229
seq_824_test seq_7096_train 0.97 0.98 95.9 93.41 1.88e-236
seq_1294_test seq_61_train 0.98 0.98 95.1 93.39 5.84e-232
seq_1655_test seq_3707_train 0.98 0.99 94.9 93.38 4.82e-230
seq_1153_test seq_523_train 0.98 0.99 94.7 93.18 9.07e-229
seq_882_test seq_9178_train 0.99 0.99 94.5 93.18 1.89e-228
seq_1789_test seq_4331_train 0.99 1.00 94.1 93.16 3.53e-227
seq_2354_test seq_2525_train 1.00 0.99 93.7 93.14 1.07e-223
seq_1614_test seq_6166_train 0.97 0.97 96.2 93.12 4.26e-237
seq_882_test seq_6087_train 0.97 0.97 95.8 93.12 1.59e-234
seq_304_test seq_9467_train 0.98 0.99 94.5 92.99 1.21e-224
seq_137_test seq_8971_train 0.99 0.99 94.1 92.97 2.82e-225
seq_2072_test seq_10386_train 0.99 0.99 93.7 92.95 2.22e-223
seq_722_test seq_8582_train 0.97 0.97 95.8 92.93 1.59e-234
seq_164_test seq_2557_train 0.97 0.97 95.6 92.92 1.46e-233
seq_824_test seq_7488_train 0.97 0.98 95.9 92.83 3.94e-236
seq_3062_test seq_10222_train 0.99 0.99 93.7 92.76 1.97e-222
seq_1732_test seq_3940_train 0.96 0.96 97.0 92.73 1.11e-239
seq_708_test seq_6467_train 0.98 0.99 94.3 92.60 7.33e-227
seq_2901_test seq_1638_train 0.98 0.98 94.3 92.60 5.84e-225
seq_210_test seq_7930_train 0.99 0.98 94.1 92.59 5.19e-224
seq_3194_test seq_6795_train 0.96 0.96 96.8 92.54 4.59e-238
seq_1506_test seq_9229_train 0.98 0.98 94.6 92.52 1.70e-227
seq_1576_test seq_10123_train 0.98 0.98 94.1 92.41 4.06e-222
seq_3058_test seq_10386_train 0.99 0.98 93.7 92.20 3.13e-220
seq_407_test seq_6600_train 0.99 0.99 93.1 92.17 4.90e-218
seq_3016_test seq_7554_train 0.97 0.97 95.4 92.16 4.82e-230
seq_1622_test seq_1289_train 1.00 0.99 93.0 92.07 3.13e-220
seq_3004_test seq_9744_train 1.00 0.99 93.1 91.98 3.13e-220
seq_407_test seq_299_train 0.99 0.99 92.9 91.97 1.79e-216
seq_708_test seq_4053_train 0.97 0.98 94.3 91.85 2.51e-224
seq_1504_test seq_9990_train 0.99 0.98 93.7 91.83 5.84e-225
seq_1101_test seq_2981_train 0.99 0.98 93.7 91.83 8.38e-222
seq_2412_test seq_9450_train 0.99 0.99 92.9 91.79 7.51e-216
seq_565_test seq_5727_train 0.99 0.99 92.7 91.77 1.32e-214
seq_1090_test seq_4871_train 0.97 0.96 95.2 91.77 1.52e-226
seq_1904_test seq_1200_train 0.95 0.95 96.8 91.77 7.61e-235
seq_137_test seq_8799_train 1.00 1.00 92.1 91.73 4.01e-212
seq_1278_test seq_5834_train 0.97 0.99 94.1 91.65 1.36e-225
seq_1090_test seq_6031_train 0.96 0.96 95.8 91.58 2.09e-229
seq_824_test seq_9278_train 0.95 0.95 96.4 91.58 6.40e-233
seq_710_test seq_6166_train 0.96 0.96 95.0 91.58 3.16e-226
seq_1506_test seq_10084_train 0.97 0.97 94.4 91.57 9.51e-223
seq_1805_test seq_4204_train 0.97 0.97 94.4 91.57 9.51e-223
seq_1446_test seq_1672_train 1.00 0.99 92.3 91.56 2.70e-214
seq_832_test seq_8984_train 1.00 0.99 92.8 91.50 1.16e-218
seq_708_test seq_9450_train 0.97 0.97 94.6 91.38 2.51e-224
seq_1692_test seq_8927_train 0.97 0.97 94.4 91.38 4.06e-222
seq_540_test seq_7935_train 0.96 0.96 95.0 91.20 1.07e-223
seq_137_test seq_2231_train 0.94 0.94 96.6 91.19 1.34e-232
seq_407_test seq_7792_train 0.97 0.97 94.0 91.18 5.63e-219
seq_1622_test seq_9377_train 0.98 0.97 93.6 91.17 1.01e-217
seq_2468_test seq_7943_train 1.00 1.00 91.3 91.12 3.41e-207
seq_3126_test seq_1200_train 0.98 0.99 92.9 91.04 4.01e-212
seq_824_test seq_4264_train 0.95 0.96 95.8 91.01 2.31e-230
seq_2648_test seq_705_train 0.97 0.99 93.5 90.88 1.52e-220
seq_407_test seq_5134_train 0.99 0.98 92.3 90.82 2.41e-209
seq_3271_test seq_10347_train 0.97 0.97 94.0 90.80 1.01e-217
seq_1094_test seq_1104_train 0.94 0.94 96.8 90.80 2.79e-232
seq_2468_test seq_9467_train 0.97 0.97 93.2 90.78 2.31e-213
seq_3016_test seq_9947_train 0.96 0.96 94.9 90.72 1.07e-223
seq_2906_test seq_6614_train 0.94 0.94 96.1 90.72 2.09e-229
seq_1294_test seq_9744_train 0.99 0.98 92.3 90.64 4.01e-212
seq_639_test seq_8094_train 0.99 0.98 92.3 90.64 4.01e-212
seq_2468_test seq_5096_train 1.00 1.00 91.0 90.64 7.83e-204
seq_5367_test seq_10667_train 0.97 0.95 95.8 90.63 1.59e-234
seq_1341_test seq_4673_train 0.98 0.98 92.2 90.54 5.82e-210
seq_1364_test seq_7792_train 0.96 0.96 94.5 90.53 2.74e-219
seq_899_test seq_11054_train 0.98 0.99 92.3 90.45 5.82e-210
seq_2648_test seq_4673_train 0.97 0.98 93.0 90.40 2.31e-213
seq_496_test seq_449_train 0.98 0.98 92.4 90.37 1.18e-209
seq_1965_test seq_9030_train 0.95 0.95 94.9 90.34 1.97e-222
seq_304_test seq_7943_train 0.96 0.96 94.1 90.34 2.07e-217
seq_304_test seq_5096_train 0.96 0.96 93.9 90.33 1.54e-215
seq_137_test seq_7634_train 0.95 0.95 95.3 90.15 4.60e-223
seq_1364_test seq_4297_train 0.96 0.96 94.1 90.15 2.07e-217
seq_722_test seq_4850_train 0.96 0.96 93.7 90.14 3.66e-216
seq_304_test seq_7630_train 0.96 0.97 93.7 90.14 6.45e-215