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 enhancers_test.csv.gz against train set enhancers_train.csv.gz
Data Leakage:!WarningHow a flag is decided →
gb-qc v1.0.0 · run 2026-09-15 22:31:12

Basic Descriptive Statistics

Filename enhancers_test.csv.gz enhancers_train.csv.gz
Number of sequences 3000 30000
Minimum length 400 400
Mean length 400.00 400.00
Maximum length 400 400
!

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 enhancers_test.csv.gz enhancers_train.csv.gz
Data Leakage (percentage) 1.50% 0.24%
Data Leakage (count) 45 71
Similarity Histogram
80 high-similarity alignments
Query (Q) Target (T) Q Cov. T Cov. % Identity % Similarity E-value Alignment
seq_868_test seq_24889_train 0.99 0.99 98.2 97.71 1.10e-207
seq_1663_test seq_21191_train 1.00 1.00 97.2 97.20 2.17e-202
seq_1122_test seq_29985_train 1.00 1.00 97.0 97.00 9.65e-201
seq_1174_test seq_11836_train 0.99 0.99 97.2 96.52 2.06e-200
seq_2987_test seq_22383_train 0.98 0.98 97.9 95.94 4.64e-202
seq_1196_test seq_27090_train 0.98 0.98 97.4 95.74 1.85e-197
seq_868_test seq_24357_train 0.97 0.97 98.2 95.55 9.92e-202
seq_1750_test seq_9940_train 0.98 0.98 97.4 95.45 9.04e-199
seq_2324_test seq_3716_train 0.98 0.99 96.9 95.45 3.77e-196
seq_1750_test seq_845_train 0.99 0.99 96.2 95.24 3.25e-193
seq_2180_test seq_15880_train 1.00 1.00 95.2 95.20 2.54e-189
seq_301_test seq_24271_train 0.98 0.98 97.1 95.16 3.94e-197
seq_2953_test seq_21436_train 0.97 0.97 98.4 95.15 4.64e-202
seq_2324_test seq_6217_train 0.98 0.99 96.4 94.95 6.88e-193
seq_1447_test seq_12906_train 0.99 0.99 95.4 94.92 1.21e-189
seq_2324_test seq_16737_train 0.99 1.00 95.4 94.92 5.35e-189
seq_1110_test seq_24889_train 0.99 0.99 95.2 94.72 4.98e-188
seq_2924_test seq_17348_train 0.97 0.97 97.1 94.67 8.01e-196
seq_2478_test seq_7018_train 0.99 0.99 95.2 94.53 2.20e-187
seq_301_test seq_14071_train 0.99 0.99 95.2 94.53 2.20e-187
seq_2982_test seq_12687_train 0.98 0.98 96.6 94.47 3.25e-193
seq_1493_test seq_21191_train 0.97 0.96 97.9 94.47 1.85e-197
seq_392_test seq_18830_train 1.00 0.99 95.0 94.33 4.62e-187
seq_301_test seq_23036_train 0.98 0.98 95.9 94.27 1.21e-189
seq_2982_test seq_619_train 0.97 0.97 96.9 93.99 6.88e-193
seq_49_test seq_25432_train 0.98 0.98 95.9 93.98 5.35e-189
seq_2619_test seq_29985_train 0.98 0.98 95.6 93.97 4.98e-188
seq_1515_test seq_29985_train 0.98 0.98 95.6 93.97 4.98e-188
seq_2276_test seq_17419_train 0.99 0.99 94.9 93.76 1.72e-184
seq_392_test seq_20954_train 0.98 0.98 95.1 93.48 8.22e-185
seq_2178_test seq_24714_train 0.98 0.97 95.6 93.21 3.93e-185
seq_1802_test seq_2657_train 0.99 0.98 95.2 93.11 1.05e-187
seq_2276_test seq_20127_train 0.99 0.99 93.4 92.93 7.55e-177
seq_1622_test seq_15880_train 0.95 0.95 97.6 92.92 3.25e-193
seq_2982_test seq_20663_train 0.98 0.98 94.4 92.80 5.10e-180
seq_1699_test seq_26535_train 0.99 0.99 93.4 92.75 1.38e-175
seq_1110_test seq_24357_train 0.97 0.97 95.3 92.73 7.53e-184
seq_2843_test seq_21436_train 0.96 0.96 96.8 92.64 5.73e-190
seq_1181_test seq_11836_train 0.95 0.95 97.3 92.63 1.37e-191
seq_1301_test seq_24147_train 1.00 1.00 92.7 92.51 9.34e-173
seq_1763_test seq_28098_train 0.96 0.96 96.1 92.45 4.27e-186
seq_1532_test seq_28319_train 0.95 0.95 97.1 92.44 5.73e-190
seq_907_test seq_14364_train 0.98 0.97 94.8 92.24 2.45e-180
seq_2500_test seq_28697_train 0.98 0.97 94.6 92.23 4.58e-179
seq_301_test seq_25086_train 0.97 0.97 94.6 92.23 1.06e-179
seq_1763_test seq_9623_train 0.94 0.94 97.6 92.23 2.89e-191
seq_8_test seq_19920_train 0.98 0.98 94.3 92.23 7.55e-177
seq_1328_test seq_27622_train 0.97 0.97 94.6 92.05 4.58e-179
seq_1236_test seq_19756_train 0.93 0.94 98.6 91.99 7.26e-194
seq_392_test seq_16776_train 0.99 0.99 92.9 91.97 8.13e-172
seq_2276_test seq_15198_train 0.96 0.96 95.8 91.97 7.53e-184
seq_1622_test seq_29778_train 0.96 0.96 95.3 91.96 6.25e-182
seq_1459_test seq_17884_train 0.97 0.97 94.8 91.96 5.10e-180
seq_392_test seq_23566_train 0.98 0.98 93.8 91.74 1.38e-175
seq_1802_test seq_6063_train 0.98 0.98 93.1 91.70 9.34e-173
seq_1358_test seq_6540_train 0.99 1.00 92.7 91.59 2.20e-173
seq_1358_test seq_26105_train 0.99 1.00 92.7 91.59 2.20e-173
seq_494_test seq_13185_train 0.96 0.97 94.8 91.48 5.65e-181
seq_1301_test seq_7026_train 0.98 0.98 92.8 91.22 1.44e-170
seq_1301_test seq_18526_train 0.98 0.98 92.6 91.21 1.24e-169
seq_2112_test seq_28447_train 0.99 0.98 92.4 91.01 3.21e-166
seq_494_test seq_26682_train 0.96 0.97 94.3 91.00 8.49e-178
seq_924_test seq_28492_train 0.94 0.94 96.8 90.99 7.53e-184
seq_1358_test seq_29621_train 0.96 0.97 94.6 90.82 4.58e-179
seq_1196_test seq_16138_train 0.94 0.94 96.8 90.80 7.53e-184
seq_2987_test seq_24188_train 0.94 0.94 96.8 90.51 3.29e-183
seq_49_test seq_26857_train 0.95 0.95 95.0 90.44 1.56e-176
seq_1763_test seq_29642_train 0.97 0.96 94.0 90.43 4.54e-173
seq_2276_test seq_20099_train 0.95 0.95 95.0 90.25 1.56e-176
seq_1459_test seq_14315_train 0.95 0.95 95.0 90.25 1.56e-176
seq_2982_test seq_21872_train 0.98 0.98 91.8 90.24 2.27e-164
seq_2276_test seq_29411_train 0.97 0.96 93.8 90.24 5.19e-174
seq_428_test seq_19347_train 0.94 0.94 96.5 90.23 2.45e-180
seq_385_test seq_19347_train 0.94 0.94 96.5 90.23 2.45e-180
seq_1236_test seq_5231_train 0.98 0.98 91.6 90.23 1.90e-163
seq_1663_test seq_16157_train 0.93 0.93 97.0 90.21 1.57e-183
seq_2804_test seq_17077_train 1.00 1.00 90.2 90.20 5.82e-158
seq_1328_test seq_6908_train 0.95 0.95 94.7 90.15 1.38e-175
seq_8_test seq_13410_train 0.94 0.94 95.7 90.15 9.51e-179
seq_2783_test seq_596_train 0.98 1.00 91.7 90.14 6.53e-166