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 promoter_detection_300_notata_val.csv.gz against train set promoter_detection_300_notata_train.csv.gz
Data Leakage:!WarningHow a flag is decided →
gb-qc v1.0.0 · run 2026-09-15 22:30:59

Basic Descriptive Statistics

Filename promoter_detection_300_notata_val.csv.gz promoter_detection_300_notata_train.csv.gz
Number of sequences 5307 42452
Minimum length 300 300
Mean length 300.00 300.00
Maximum length 300 300
!

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 promoter_detection_300_notata_val.csv.gz promoter_detection_300_notata_train.csv.gz
Data Leakage (percentage) 1.04% 0.16%
Data Leakage (count) 55 67
Similarity Histogram
69 high-similarity alignments
Query (Q) Target (T) Q Cov. T Cov. % Identity % Similarity E-value Alignment
seq_2744_test seq_30967_train 1.00 1.00 100.0 100.00 3.72e-164
seq_3843_test seq_462_train 1.00 1.00 100.0 100.00 3.72e-164
seq_1622_test seq_2033_train 1.00 1.00 100.0 100.00 3.72e-164
seq_3049_test seq_30541_train 1.00 1.00 100.0 100.00 3.72e-164
seq_81_test seq_19190_train 1.00 1.00 100.0 100.00 3.72e-164
seq_3771_test seq_3140_train 1.00 1.00 100.0 100.00 3.72e-164
seq_1907_test seq_9773_train 1.00 1.00 100.0 100.00 3.72e-164
seq_1939_test seq_8519_train 1.00 1.00 100.0 100.00 3.72e-164
seq_2917_test seq_34301_train 1.00 1.00 100.0 100.00 3.72e-164
seq_4619_test seq_1617_train 1.00 1.00 100.0 100.00 3.72e-164
seq_2674_test seq_9160_train 1.00 1.00 100.0 100.00 3.72e-164
seq_1517_test seq_6228_train 1.00 1.00 100.0 100.00 3.72e-164
seq_5216_test seq_35325_train 1.00 1.00 100.0 100.00 3.72e-164
seq_4231_test seq_19943_train 1.00 1.00 100.0 100.00 3.72e-164
seq_4157_test seq_29367_train 1.00 1.00 100.0 100.00 3.72e-164
seq_5063_test seq_23062_train 1.00 1.00 100.0 100.00 3.72e-164
seq_1024_test seq_21124_train 1.00 1.00 100.0 100.00 3.72e-164
seq_2426_test seq_8979_train 1.00 1.00 100.0 100.00 3.72e-164
seq_1208_test seq_38968_train 1.00 1.00 100.0 99.70 1.77e-163
seq_2508_test seq_9090_train 1.00 1.00 99.6 99.60 1.82e-162
seq_2050_test seq_16409_train 1.00 1.00 99.6 99.60 1.82e-162
seq_4050_test seq_38800_train 1.00 1.00 99.3 99.30 8.79e-161
seq_4050_test seq_30072_train 1.00 1.00 99.3 99.30 8.79e-161
seq_4248_test seq_31511_train 1.00 1.00 99.3 99.30 8.79e-161
seq_2822_test seq_40212_train 0.99 0.99 100.0 99.30 8.36e-163
seq_1904_test seq_26225_train 0.99 0.99 100.0 99.00 3.95e-162
seq_2946_test seq_635_train 0.99 0.99 100.0 99.00 3.95e-162
seq_1209_test seq_20763_train 1.00 1.00 99.0 99.00 4.21e-159
seq_3816_test seq_33934_train 1.00 1.00 99.0 99.00 4.21e-159
seq_1209_test seq_24942_train 1.00 1.00 98.9 98.60 1.97e-158
seq_4064_test seq_4122_train 1.00 1.00 98.6 98.60 2.00e-157
seq_3771_test seq_25908_train 0.98 0.98 100.0 98.30 8.79e-161
seq_264_test seq_12918_train 0.98 0.98 100.0 98.30 8.79e-161
seq_847_test seq_8928_train 0.98 0.98 100.0 98.30 8.79e-161
seq_1391_test seq_23007_train 1.00 1.00 98.3 98.01 2.02e-154
seq_3615_test seq_13439_train 1.00 1.00 98.0 98.00 4.35e-154
seq_24_test seq_31707_train 0.98 0.98 100.0 98.00 4.14e-160
seq_3203_test seq_28518_train 0.98 0.98 100.0 97.70 1.94e-159
seq_5297_test seq_22204_train 0.97 0.97 100.0 97.00 4.27e-158
seq_5234_test seq_11736_train 0.97 0.97 100.0 97.00 4.27e-158
seq_5216_test seq_28514_train 0.97 0.97 100.0 97.00 4.27e-158
seq_4690_test seq_41222_train 1.00 1.00 96.6 96.60 1.81e-147
seq_2946_test seq_15617_train 0.96 0.96 100.0 96.30 9.32e-157
seq_1622_test seq_42249_train 0.96 0.96 100.0 96.30 9.32e-157
seq_2889_test seq_31536_train 0.96 0.96 100.0 96.30 9.32e-157
seq_5297_test seq_25836_train 0.96 0.96 100.0 96.30 9.32e-157
seq_3157_test seq_32863_train 0.96 0.96 100.0 96.30 9.32e-157
seq_5297_test seq_2465_train 0.96 0.96 99.6 95.91 4.35e-155
seq_1238_test seq_21580_train 0.99 0.99 96.2 94.95 3.30e-143
seq_461_test seq_143_train 0.94 0.94 100.0 94.30 9.31e-153
seq_2212_test seq_7202_train 0.94 0.94 100.0 93.70 1.98e-151
seq_80_test seq_28870_train 0.94 0.94 100.0 93.70 1.98e-151
seq_3002_test seq_29408_train 0.94 0.94 100.0 93.70 1.98e-151
seq_3865_test seq_21580_train 0.99 0.99 94.9 93.67 9.98e-137
seq_2347_test seq_12999_train 0.93 0.93 100.0 93.30 9.09e-151
seq_2485_test seq_27172_train 0.93 0.93 100.0 93.30 9.09e-151
seq_2485_test seq_19067_train 0.93 0.93 100.0 93.30 9.09e-151
seq_264_test seq_11903_train 0.93 0.93 100.0 93.00 4.17e-150
seq_1607_test seq_32863_train 0.93 0.93 100.0 92.70 1.91e-149
seq_4690_test seq_17577_train 0.96 0.96 96.8 92.64 1.32e-140
seq_2177_test seq_39290_train 0.92 0.92 100.0 92.30 8.73e-149
seq_4690_test seq_6030_train 0.95 0.95 96.8 91.96 2.62e-139
seq_3269_test seq_9426_train 0.92 0.92 100.0 91.70 1.81e-147
seq_3144_test seq_20942_train 0.92 0.92 100.0 91.70 1.81e-147
seq_2177_test seq_24836_train 0.92 0.92 100.0 91.70 1.81e-147
seq_4889_test seq_19452_train 0.91 0.91 100.0 91.30 8.25e-147
seq_1238_test seq_23513_train 0.94 0.94 96.4 90.62 9.19e-136
seq_1385_test seq_6867_train 1.00 0.98 91.9 90.34 2.02e-119
seq_648_test seq_3272_train 0.90 0.90 100.0 90.00 3.46e-144