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_test.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 22:30:51

Basic Descriptive Statistics

Filename core_promoter_detection_notata_test.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_test.csv.gz core_promoter_detection_notata_train.csv.gz
Data Leakage (percentage) 1.13% 0.16%
Data Leakage (count) 60 69
Similarity Histogram
72 high-similarity alignments
Query (Q) Target (T) Q Cov. T Cov. % Identity % Similarity E-value Alignment
seq_297_test seq_20590_train 1.00 1.00 100.0 100.00 1.41e-34
seq_721_test seq_24263_train 1.00 1.00 100.0 100.00 1.41e-34
seq_972_test seq_10538_train 1.00 1.00 100.0 100.00 1.41e-34
seq_3032_test seq_38277_train 1.00 1.00 100.0 100.00 1.41e-34
seq_2056_test seq_8749_train 1.00 1.00 100.0 100.00 1.41e-34
seq_274_test seq_9948_train 1.00 1.00 100.0 100.00 1.41e-34
seq_3924_test seq_39322_train 1.00 1.00 100.0 100.00 1.41e-34
seq_1139_test seq_31338_train 1.00 1.00 100.0 100.00 1.41e-34
seq_2794_test seq_10528_train 1.00 1.00 100.0 100.00 1.41e-34
seq_2167_test seq_27469_train 1.00 1.00 100.0 100.00 1.41e-34
seq_3070_test seq_3865_train 1.00 1.00 100.0 100.00 1.41e-34
seq_3365_test seq_2144_train 1.00 1.00 100.0 100.00 1.41e-34
seq_4127_test seq_8211_train 1.00 1.00 100.0 100.00 1.41e-34
seq_4159_test seq_27469_train 1.00 1.00 100.0 100.00 1.41e-34
seq_367_test seq_33519_train 1.00 1.00 100.0 100.00 1.41e-34
seq_2828_test seq_23790_train 1.00 1.00 100.0 100.00 1.41e-34
seq_5206_test seq_3129_train 1.00 1.00 100.0 100.00 1.41e-34
seq_1162_test seq_42390_train 1.00 1.00 100.0 100.00 1.41e-34
seq_1461_test seq_31628_train 1.00 1.00 100.0 100.00 1.41e-34
seq_1808_test seq_22926_train 1.00 1.00 100.0 100.00 1.41e-34
seq_184_test seq_32751_train 1.00 1.00 100.0 100.00 1.41e-34
seq_650_test seq_32404_train 1.00 1.00 100.0 100.00 1.41e-34
seq_208_test seq_41847_train 1.00 1.00 100.0 100.00 1.41e-34
seq_1013_test seq_16391_train 1.00 1.00 100.0 100.00 1.41e-34
seq_3713_test seq_19209_train 1.00 1.00 100.0 100.00 1.41e-34
seq_2866_test seq_21614_train 1.00 1.00 100.0 100.00 1.41e-34
seq_4178_test seq_40104_train 1.00 1.00 100.0 100.00 1.41e-34
seq_1919_test seq_16757_train 1.00 1.00 100.0 100.00 1.41e-34
seq_1371_test seq_4876_train 1.00 1.00 100.0 100.00 1.41e-34
seq_1545_test seq_5555_train 1.00 1.00 100.0 100.00 1.41e-34
seq_4806_test seq_10542_train 0.99 0.99 100.0 98.60 6.91e-34
seq_4358_test seq_31884_train 0.99 0.99 100.0 98.60 6.91e-34
seq_3899_test seq_2549_train 0.99 0.99 100.0 98.60 6.91e-34
seq_3989_test seq_32676_train 1.00 1.00 98.5 98.50 7.44e-33
seq_5208_test seq_42434_train 1.00 1.00 98.5 98.50 7.44e-33
seq_1236_test seq_23242_train 0.99 0.99 98.5 97.12 3.60e-32
seq_4654_test seq_16525_train 0.97 0.97 100.0 97.10 3.37e-33
seq_5208_test seq_3250_train 1.00 1.00 97.1 97.10 3.79e-31
seq_2982_test seq_14874_train 0.97 0.97 100.0 97.10 3.37e-33
seq_3804_test seq_12224_train 1.00 1.00 97.1 97.10 3.79e-31
seq_2519_test seq_37514_train 1.00 1.00 97.1 97.10 3.79e-31
seq_4654_test seq_218_train 0.99 1.00 97.1 95.74 8.58e-30
seq_3804_test seq_34900_train 0.99 0.99 97.1 95.74 1.81e-30
seq_940_test seq_41028_train 0.96 0.96 100.0 95.70 1.64e-32
seq_2711_test seq_33898_train 1.00 1.00 95.7 95.70 1.86e-29
seq_3824_test seq_28177_train 0.96 0.96 100.0 95.70 1.64e-32
seq_4178_test seq_24097_train 1.00 1.00 95.7 95.70 1.86e-29
seq_2550_test seq_35570_train 0.97 0.97 98.5 95.64 1.73e-31
seq_3072_test seq_34595_train 0.94 0.94 100.0 94.30 7.91e-32
seq_3072_test seq_12318_train 0.94 0.94 100.0 94.30 7.91e-32
seq_189_test seq_12064_train 0.94 0.94 100.0 94.30 7.91e-32
seq_3804_test seq_23718_train 0.96 0.96 98.5 94.26 8.29e-31
seq_4984_test seq_7195_train 0.99 0.99 95.6 94.26 8.74e-29
seq_892_test seq_21529_train 1.00 1.00 94.2 94.20 8.77e-28
seq_2711_test seq_24774_train 1.00 1.00 94.2 94.20 8.77e-28
seq_1523_test seq_37478_train 1.00 1.00 94.2 94.20 8.77e-28
seq_4943_test seq_10478_train 1.00 1.00 94.2 94.20 8.77e-28
seq_892_test seq_15662_train 0.97 0.97 97.0 94.19 8.58e-30
seq_972_test seq_10203_train 0.93 0.93 100.0 92.90 3.79e-31
seq_1734_test seq_16420_train 0.93 0.93 100.0 92.90 3.79e-31
seq_321_test seq_10056_train 0.97 1.00 94.2 91.47 3.79e-25
seq_321_test seq_15513_train 0.97 1.00 94.2 91.47 3.79e-25
seq_2451_test seq_20442_train 0.93 0.93 98.4 91.41 1.86e-29
seq_4955_test seq_21529_train 1.00 1.00 91.4 91.40 1.69e-24
seq_2309_test seq_15860_train 1.00 1.00 91.4 91.40 1.69e-24
seq_3069_test seq_3491_train 0.91 0.91 100.0 91.40 1.81e-30
seq_1882_test seq_6730_train 0.99 0.99 91.3 90.02 7.50e-24
seq_19_test seq_34905_train 0.93 0.93 96.9 90.02 8.77e-28
seq_4756_test seq_25798_train 0.90 0.90 100.0 90.00 8.58e-30
seq_698_test seq_25798_train 0.90 0.90 100.0 90.00 8.58e-30
seq_1882_test seq_24028_train 1.00 1.00 90.0 90.00 6.89e-23
seq_1371_test seq_6595_train 1.00 1.00 90.0 90.00 6.89e-23