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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 enhancer_promoter_interaction_NHEK_test.csv.gz against train set enhancer_promoter_interaction_NHEK_train.csv.gz
Data Leakage:!WarningHow a flag is decided →
gb-qc v1.0.0 · run 2026-09-15 22:31:13

Basic Descriptive Statistics

Filename enhancer_promoter_interaction_NHEK_test.csv.gz enhancer_promoter_interaction_NHEK_train.csv.gz
Number of sequences 2000 10000
Minimum length 5000 5000
Mean length 5000.00 5000.00
Maximum length 5000 5000

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 enhancer_promoter_interaction_NHEK_test.csv.gz enhancer_promoter_interaction_NHEK_train.csv.gz
Data Leakage (percentage) 1.95% 0.39%
Data Leakage (count) 39 39
Similarity Histogram
39 high-similarity alignments
Query (Q) Target (T) Q Cov. T Cov. % Identity % Similarity E-value Alignment
seq_601_test seq_5286_train 0.99 0.99 99.5 98.50 0.00e+00
seq_1704_test seq_1728_train 0.99 0.99 99.5 98.50 0.00e+00
seq_779_test seq_4745_train 0.99 0.99 99.5 98.50 0.00e+00
seq_1399_test seq_7945_train 0.99 0.99 99.5 98.50 0.00e+00
seq_1939_test seq_3981_train 0.99 0.99 99.4 98.41 0.00e+00
seq_731_test seq_8353_train 0.99 0.99 99.4 98.41 0.00e+00
seq_236_test seq_5276_train 0.99 0.99 99.4 98.41 0.00e+00
seq_327_test seq_1194_train 0.99 0.99 99.4 98.41 0.00e+00
seq_941_test seq_3364_train 0.99 0.99 99.4 98.41 0.00e+00
seq_208_test seq_5304_train 0.99 0.99 99.4 98.41 0.00e+00
seq_711_test seq_613_train 0.99 0.99 99.4 98.41 0.00e+00
seq_355_test seq_6978_train 0.99 0.99 99.4 98.41 0.00e+00
seq_156_test seq_8709_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1533_test seq_1328_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1565_test seq_9458_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1660_test seq_1585_train 0.99 0.99 99.4 98.41 0.00e+00
seq_444_test seq_4289_train 0.99 0.99 99.4 98.41 0.00e+00
seq_508_test seq_8437_train 0.99 0.99 99.4 98.41 0.00e+00
seq_88_test seq_8756_train 0.99 0.99 99.4 98.41 0.00e+00
seq_463_test seq_6946_train 0.99 0.99 99.4 98.41 0.00e+00
seq_66_test seq_7657_train 0.99 0.99 99.4 98.41 0.00e+00
seq_35_test seq_737_train 0.99 0.99 99.4 98.41 0.00e+00
seq_662_test seq_9161_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1080_test seq_9666_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1499_test seq_7613_train 0.99 0.99 99.4 98.41 0.00e+00
seq_1108_test seq_3173_train 0.99 0.99 99.3 98.31 0.00e+00
seq_1923_test seq_4725_train 0.99 0.99 99.3 98.31 0.00e+00
seq_1220_test seq_381_train 0.99 0.99 99.3 98.31 0.00e+00
seq_111_test seq_6491_train 0.99 0.99 99.3 98.31 0.00e+00
seq_1573_test seq_2884_train 0.99 0.99 99.3 98.31 0.00e+00
seq_1903_test seq_4542_train 0.99 0.99 99.3 98.31 0.00e+00
seq_1929_test seq_2445_train 0.99 0.99 99.3 98.31 0.00e+00
seq_1961_test seq_9694_train 0.99 0.99 99.3 98.31 0.00e+00
seq_1508_test seq_3999_train 0.99 0.99 99.2 98.21 0.00e+00
seq_1988_test seq_2567_train 0.99 0.99 99.2 98.21 0.00e+00
seq_78_test seq_1970_train 0.99 0.99 99.2 98.21 0.00e+00
seq_1467_test seq_9928_train 0.99 0.99 99.2 98.21 0.00e+00
seq_305_test seq_5945_train 0.98 0.98 99.0 97.02 0.00e+00
seq_844_test seq_3769_train 0.96 0.96 98.4 94.46 0.00e+00