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 core_promoter_detection_notata_val.csv.gz against train set core_promoter_detection_notata_train.csv.gz
Data Leakage:!WarningHow a flag is decided →
gb-qc v1.0.0 · run 2026-09-15 22:30:33

Basic Descriptive Statistics

Filename core_promoter_detection_notata_val.csv.gz core_promoter_detection_notata_train.csv.gz
Number of sequences 5307 42452
Minimum length 70 70
Mean length 70.00 70.00
Maximum length 70 70
!

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 core_promoter_detection_notata_val.csv.gz core_promoter_detection_notata_train.csv.gz
Data Leakage (percentage) 1.11% 0.16%
Data Leakage (count) 59 66
Similarity Histogram
72 high-similarity alignments
Query (Q) Target (T) Q Cov. T Cov. % Identity % Similarity E-value Alignment
seq_1381_test seq_21816_train 1.00 1.00 100.0 100.00 1.41e-34
seq_4337_test seq_2399_train 1.00 1.00 100.0 100.00 1.41e-34
seq_2611_test seq_33323_train 1.00 1.00 100.0 100.00 1.41e-34
seq_2589_test seq_382_train 1.00 1.00 100.0 100.00 1.41e-34
seq_3616_test seq_30273_train 1.00 1.00 100.0 100.00 1.41e-34
seq_2895_test seq_18537_train 1.00 1.00 100.0 100.00 1.41e-34
seq_4861_test seq_41293_train 1.00 1.00 100.0 100.00 1.41e-34
seq_2228_test seq_8644_train 1.00 1.00 100.0 100.00 1.41e-34
seq_5267_test seq_18910_train 1.00 1.00 100.0 100.00 1.41e-34
seq_3714_test seq_27358_train 1.00 1.00 100.0 100.00 1.41e-34
seq_1508_test seq_18284_train 1.00 1.00 100.0 100.00 1.41e-34
seq_860_test seq_12306_train 1.00 1.00 100.0 100.00 1.41e-34
seq_1475_test seq_34_train 1.00 1.00 100.0 100.00 1.41e-34
seq_4576_test seq_4621_train 1.00 1.00 100.0 100.00 1.41e-34
seq_2411_test seq_3063_train 1.00 1.00 100.0 100.00 1.41e-34
seq_3235_test seq_31659_train 1.00 1.00 100.0 100.00 1.41e-34
seq_3912_test seq_14098_train 1.00 1.00 100.0 100.00 1.41e-34
seq_3163_test seq_167_train 1.00 1.00 100.0 100.00 1.41e-34
seq_3772_test seq_1841_train 1.00 1.00 100.0 100.00 1.41e-34
seq_3954_test seq_8388_train 1.00 1.00 100.0 100.00 1.41e-34
seq_3954_test seq_13221_train 1.00 1.00 100.0 100.00 1.41e-34
seq_3954_test seq_33567_train 1.00 1.00 100.0 100.00 1.41e-34
seq_4114_test seq_17643_train 1.00 1.00 100.0 100.00 1.41e-34
seq_2614_test seq_19093_train 1.00 1.00 100.0 100.00 1.41e-34
seq_2243_test seq_19596_train 1.00 1.00 100.0 100.00 1.41e-34
seq_4234_test seq_2006_train 1.00 1.00 100.0 100.00 1.41e-34
seq_5042_test seq_28910_train 1.00 1.00 100.0 100.00 1.41e-34
seq_4705_test seq_32152_train 1.00 1.00 100.0 100.00 1.41e-34
seq_1703_test seq_40711_train 1.00 1.00 100.0 100.00 1.41e-34
seq_914_test seq_8740_train 1.00 1.00 100.0 100.00 1.41e-34
seq_2393_test seq_5531_train 1.00 1.00 100.0 100.00 1.41e-34
seq_272_test seq_32085_train 1.00 1.00 98.5 98.50 7.44e-33
seq_5267_test seq_17339_train 1.00 1.00 98.5 98.50 7.44e-33
seq_1888_test seq_8305_train 1.00 1.00 98.5 98.50 7.44e-33
seq_2630_test seq_29884_train 1.00 1.00 98.5 98.50 7.44e-33
seq_576_test seq_8740_train 1.00 1.00 98.5 98.50 7.44e-33
seq_1092_test seq_16539_train 1.00 1.00 98.5 98.50 7.44e-33
seq_1175_test seq_693_train 1.00 1.00 98.5 98.50 7.44e-33
seq_3616_test seq_19175_train 0.99 0.99 98.5 97.12 3.60e-32
seq_4372_test seq_11546_train 1.00 1.00 97.1 97.10 3.79e-31
seq_4861_test seq_6127_train 0.97 0.97 100.0 97.10 3.37e-33
seq_1506_test seq_14098_train 1.00 1.00 97.1 97.10 3.79e-31
seq_4618_test seq_24166_train 1.00 1.00 95.7 95.70 1.86e-29
seq_4562_test seq_37514_train 1.00 1.00 95.7 95.70 1.86e-29
seq_569_test seq_29422_train 0.96 0.96 100.0 95.70 1.64e-32
seq_1723_test seq_18737_train 0.94 0.94 100.0 94.30 7.91e-32
seq_3616_test seq_8532_train 0.99 0.99 95.6 94.26 8.74e-29
seq_4091_test seq_24708_train 1.00 1.00 94.2 94.20 8.77e-28
seq_4618_test seq_15419_train 1.00 1.00 94.2 94.20 8.77e-28
seq_4912_test seq_24708_train 1.00 1.00 94.2 94.20 8.77e-28
seq_1438_test seq_462_train 1.00 1.00 94.2 94.20 8.77e-28
seq_61_test seq_3137_train 0.93 0.93 100.0 92.90 3.79e-31
seq_61_test seq_35751_train 0.93 0.93 100.0 92.90 3.79e-31
seq_3576_test seq_23994_train 1.00 1.00 92.8 92.80 3.95e-26
seq_2830_test seq_10668_train 0.96 1.00 95.7 91.58 8.74e-29
seq_3576_test seq_30633_train 0.99 1.00 92.8 91.50 8.02e-25
seq_5214_test seq_6820_train 0.93 0.93 98.4 91.41 1.86e-29
seq_4161_test seq_24028_train 1.00 1.00 91.4 91.40 1.69e-24
seq_5288_test seq_4034_train 1.00 1.00 91.4 91.40 1.69e-24
seq_5288_test seq_15558_train 1.00 1.00 91.4 91.40 1.69e-24
seq_5288_test seq_32509_train 1.00 1.00 91.4 91.40 1.69e-24
seq_112_test seq_21529_train 1.00 1.00 91.4 91.40 1.69e-24
seq_965_test seq_8685_train 1.00 1.00 91.4 91.40 1.69e-24
seq_1828_test seq_35133_train 0.94 0.94 96.9 91.38 1.89e-28
seq_1438_test seq_24166_train 0.94 0.94 96.9 91.38 1.89e-28
seq_3592_test seq_8685_train 0.97 0.97 94.1 91.37 1.85e-26
seq_2845_test seq_16272_train 1.00 1.00 90.1 90.10 5.46e-21
seq_5053_test seq_8685_train 0.96 0.94 95.5 90.06 3.95e-26
seq_667_test seq_258_train 0.93 0.93 96.9 90.02 8.77e-28
seq_1266_test seq_12107_train 0.90 0.90 100.0 90.00 8.58e-30
seq_3576_test seq_33739_train 1.00 1.00 90.0 90.00 6.89e-23
seq_961_test seq_3106_train 1.00 1.00 90.0 90.00 6.89e-23