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_ensembl_test.csv.gz against train set human_enhancers_ensembl_train.csv.gz
Data Leakage:✖FailHow a flag is decided →
gb-qc v1.0.0 · run 2026-09-15 22:31:11

Basic Descriptive Statistics

Filename human_enhancers_ensembl_test.csv.gz human_enhancers_ensembl_train.csv.gz
Number of sequences 30970 123872
Minimum length 2 2
Mean length 267.89 269.11
Maximum length 573 573
✖

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_ensembl_test.csv.gz human_enhancers_ensembl_train.csv.gz
Data Leakage (percentage) 37.17% 9.31%
Data Leakage (count) 11512 11527
Similarity Histogram
11529 high-similarity alignments (first 100 shown)
Query (Q) Target (T) Q Cov. T Cov. % Identity % Similarity E-value Alignment
seq_15542_test seq_70692_train 1.00 1.00 100.0 100.00 1.45e-123
seq_15574_test seq_98893_train 1.00 1.00 100.0 100.00 3.02e-82
seq_15638_test seq_97711_train 1.00 1.00 100.0 100.00 4.86e-89
seq_15702_test seq_98538_train 1.00 1.00 100.0 100.00 4.11e-197
seq_15798_test seq_106223_train 1.00 1.00 100.0 100.00 2.91e-125
seq_19107_test seq_112184_train 1.00 1.00 100.0 100.00 2.57e-134
seq_19139_test seq_100186_train 1.00 1.00 100.0 100.00 5.56e-196
seq_19203_test seq_104400_train 1.00 1.00 100.0 100.00 8.66e-70
seq_19235_test seq_79113_train 1.00 1.00 100.0 100.00 1.45e-123
seq_19299_test seq_112867_train 1.00 1.00 100.0 100.00 2.35e-70
seq_19363_test seq_101950_train 1.00 1.00 100.0 100.00 2.08e-139
seq_19205_test seq_84158_train 1.00 1.00 100.0 100.00 1.58e-127
seq_19237_test seq_69508_train 1.00 1.00 100.0 100.00 4.73e-175
seq_19269_test seq_80468_train 1.00 1.00 100.0 100.00 6.94e-75
seq_19333_test seq_96047_train 1.00 1.00 100.0 100.00 2.49e-147
seq_19397_test seq_113900_train 1.00 1.00 100.0 100.00 3.74e-193
seq_19429_test seq_85700_train 1.00 1.00 100.0 100.00 1.80e-118
seq_19461_test seq_84503_train 1.00 1.00 100.0 100.00 2.21e-156
seq_19493_test seq_92813_train 1.00 1.00 100.0 100.00 2.90e-48
seq_18880_test seq_121666_train 1.00 1.00 100.0 100.00 2.81e-250
seq_18912_test seq_121761_train 1.00 1.00 100.0 100.00 2.73e-151
seq_18944_test seq_121115_train 1.00 1.00 100.0 100.00 8.25e-199
seq_18976_test seq_72073_train 1.00 1.00 100.0 100.00 9.95e-207
seq_19040_test seq_97328_train 1.00 1.00 100.0 100.00 5.43e-29
seq_19104_test seq_89275_train 1.00 1.00 100.0 100.00 4.51e-201
seq_19136_test seq_84072_train 1.00 1.00 100.0 100.00 7.90e-169
seq_19168_test seq_105754_train 1.00 1.00 100.0 100.00 2.97e-211
seq_22772_test seq_95454_train 1.00 1.00 100.0 100.00 3.99e-64
seq_22804_test seq_72031_train 1.00 1.00 100.0 100.00 3.68e-60
seq_22836_test seq_123713_train 1.00 1.00 100.0 100.00 5.07e-106
seq_22868_test seq_96823_train 1.00 1.00 100.0 100.00 2.20e-212
seq_22932_test seq_103545_train 1.00 1.00 100.0 100.00 2.57e-134
seq_22996_test seq_114683_train 1.00 1.00 100.0 100.00 1.93e-316
seq_23028_test seq_67578_train 1.00 1.00 100.0 100.00 2.91e-125
seq_30610_test seq_111179_train 1.00 1.00 100.0 100.00 5.85e-226
seq_30674_test seq_117599_train 1.00 1.00 100.0 100.00 3.02e-82
seq_30706_test seq_96356_train 1.00 1.00 100.0 100.00 6.05e-84
seq_30770_test seq_77481_train 1.00 1.00 100.0 100.00 1.44e-93
seq_30802_test seq_123700_train 1.00 1.00 100.0 100.00 1.03e-249
seq_30834_test seq_65602_train 1.00 1.00 100.0 100.00 2.78e-78
seq_30866_test seq_72224_train 1.00 1.00 100.0 100.00 2.15e-169
seq_18867_test seq_78342_train 1.00 1.00 100.0 100.00 7.70e-182
seq_18963_test seq_91842_train 1.00 1.00 100.0 100.00 2.93e-31
seq_18995_test seq_101421_train 1.00 1.00 100.0 100.00 1.84e-148
seq_19059_test seq_77352_train 1.00 1.00 100.0 100.00 8.80e-19
seq_19123_test seq_91506_train 1.00 1.00 100.0 100.00 1.87e-24
seq_21395_test seq_110264_train 1.00 1.00 100.0 100.00 2.31e-53
seq_21459_test seq_101749_train 1.00 1.00 100.0 100.00 2.65e-220
seq_21491_test seq_106124_train 1.00 1.00 100.0 100.00 7.36e-208
seq_21523_test seq_122577_train 1.00 1.00 100.0 100.00 3.04e-267
seq_21587_test seq_110406_train 1.00 1.00 100.0 100.00 2.23e-113
seq_21619_test seq_66698_train 1.00 1.00 100.0 100.00 2.11e-238
seq_21651_test seq_121114_train 1.00 1.00 100.0 100.00 1.00e-150
seq_21683_test seq_69398_train 1.00 1.00 100.0 100.00 2.42e-160
seq_21816_test seq_73298_train 1.00 1.00 100.0 100.00 3.47e-73
seq_21848_test seq_86996_train 1.00 1.00 100.0 100.00 3.04e-14
seq_21912_test seq_74553_train 1.00 1.00 100.0 100.00 5.64e-140
seq_21944_test seq_102600_train 1.00 1.00 100.0 100.00 1.79e-161
seq_21976_test seq_99826_train 1.00 1.00 100.0 100.00 1.55e-183
seq_22008_test seq_119962_train 1.00 1.00 100.0 100.00 3.41e-189
seq_30105_test seq_105902_train 1.00 1.00 100.0 100.00 2.15e-126
seq_30137_test seq_78345_train 1.00 1.00 100.0 100.00 2.09e-182
seq_30169_test seq_71186_train 1.00 1.00 100.0 100.00 5.33e-222
seq_30201_test seq_69221_train 1.00 1.00 100.0 100.00 3.30e-116
seq_30233_test seq_93630_train 1.00 1.00 100.0 100.00 3.99e-64
seq_30265_test seq_64587_train 1.00 1.00 100.0 100.00 1.57e-50
seq_30329_test seq_108950_train 1.00 1.00 100.0 100.00 4.31e-128
seq_30361_test seq_89835_train 1.00 1.00 100.0 100.00 3.18e-129
seq_15615_test seq_120617_train 1.00 1.00 100.0 100.00 1.16e-98
seq_15679_test seq_116235_train 1.00 1.00 100.0 100.00 3.93e-167
seq_15711_test seq_71257_train 1.00 1.00 100.0 100.00 1.02e-193
seq_15871_test seq_117737_train 1.00 1.00 100.0 100.00 1.96e-221
seq_21250_test seq_70855_train 1.00 1.00 100.0 100.00 5.43e-29
seq_21346_test seq_77616_train 1.00 1.00 100.0 100.00 2.57e-134
seq_21378_test seq_111922_train 1.00 1.00 100.0 100.00 3.81e-137
seq_21442_test seq_121959_train 1.00 1.00 100.0 100.00 1.82e-204
seq_21506_test seq_62850_train 1.00 1.00 100.0 100.00 6.32e-243
seq_22067_test seq_104770_train 1.00 1.00 100.0 100.00 1.03e-137
seq_22099_test seq_64459_train 1.00 1.00 100.0 100.00 1.59e-170
seq_22131_test seq_88242_train 1.00 1.00 100.0 100.00 6.85e-191
seq_22195_test seq_120432_train 1.00 1.00 100.0 100.00 4.99e-149
seq_22259_test seq_109096_train 1.00 1.00 100.0 100.00 1.66e-200
seq_22323_test seq_74049_train 1.00 1.00 100.0 100.00 2.25e-268
seq_22817_test seq_99280_train 1.00 1.00 100.0 100.00 1.70e-187
seq_22881_test seq_81382_train 1.00 1.00 100.0 100.00 1.02e-107
seq_22913_test seq_104221_train 1.00 1.00 100.0 100.00 1.54e-252
seq_22977_test seq_75218_train 1.00 1.00 100.0 100.00 4.04e-154
seq_23009_test seq_67137_train 1.00 1.00 100.0 100.00 1.75e-230
seq_23073_test seq_120398_train 1.00 1.00 100.0 100.00 1.00e-150
seq_19080_test seq_86375_train 1.00 1.00 100.0 100.00 2.91e-168
seq_19144_test seq_90473_train 1.00 1.00 100.0 100.00 3.74e-107
seq_19208_test seq_83748_train 1.00 1.00 100.0 100.00 4.85e-218
seq_19240_test seq_92148_train 1.00 1.00 100.0 100.00 1.38e-106
seq_19272_test seq_113573_train 1.00 1.00 100.0 100.00 1.51e-196
seq_19304_test seq_96394_train 1.00 1.00 100.0 100.00 1.75e-230
seq_19368_test seq_89359_train 1.00 1.00 100.0 100.00 2.01e-152
seq_23695_test seq_107837_train 1.00 1.00 100.0 100.00 3.99e-64
seq_23727_test seq_71067_train 1.00 1.00 100.0 100.00 1.16e-51
seq_23759_test seq_64677_train 1.00 1.00 100.0 100.00 5.85e-226
seq_23823_test seq_117410_train 1.00 1.00 100.0 100.00 5.64e-140