Summary

Basic Descriptive Statistics
✖ Data Leakage
Documentation GitHub
Find the shortcut. Learn the biology.
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_tata_val.csv.gz against train set promoter_detection_300_tata_train.csv.gz
Data Leakage:✖FailHow a flag is decided →
gb-qc v1.0.0 · run 2026-09-15 22:30:51

Basic Descriptive Statistics

Filename promoter_detection_300_tata_val.csv.gz promoter_detection_300_tata_train.csv.gz
Number of sequences 613 4904
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_tata_val.csv.gz promoter_detection_300_tata_train.csv.gz
Data Leakage (percentage) 5.06% 0.67%
Data Leakage (count) 31 33
Similarity Histogram
33 high-similarity alignments
Query (Q) Target (T) Q Cov. T Cov. % Identity % Similarity E-value Alignment
seq_547_test seq_603_train 1.00 1.00 100.0 100.00 4.30e-165
seq_611_test seq_968_train 1.00 1.00 100.0 100.00 4.30e-165
seq_195_test seq_4590_train 1.00 1.00 100.0 100.00 4.30e-165
seq_269_test seq_2236_train 1.00 1.00 100.0 100.00 4.30e-165
seq_576_test seq_2070_train 1.00 1.00 100.0 100.00 4.30e-165
seq_604_test seq_499_train 1.00 1.00 100.0 100.00 4.30e-165
seq_241_test seq_4098_train 1.00 1.00 100.0 100.00 4.30e-165
seq_536_test seq_2093_train 1.00 1.00 100.0 100.00 4.30e-165
seq_268_test seq_3667_train 1.00 1.00 100.0 100.00 4.30e-165
seq_502_test seq_3886_train 1.00 1.00 100.0 100.00 4.30e-165
seq_308_test seq_4319_train 1.00 1.00 100.0 100.00 4.30e-165
seq_96_test seq_1341_train 1.00 1.00 100.0 100.00 4.30e-165
seq_564_test seq_4404_train 1.00 1.00 100.0 100.00 4.30e-165
seq_606_test seq_2002_train 1.00 1.00 100.0 100.00 4.30e-165
seq_487_test seq_3047_train 1.00 1.00 100.0 99.70 2.04e-164
seq_410_test seq_3514_train 1.00 1.00 100.0 99.70 2.04e-164
seq_424_test seq_3549_train 1.00 1.00 100.0 99.70 2.04e-164
seq_437_test seq_4313_train 1.00 1.00 100.0 99.70 2.04e-164
seq_330_test seq_1983_train 1.00 1.00 100.0 99.70 2.04e-164
seq_522_test seq_3850_train 1.00 1.00 100.0 99.70 2.04e-164
seq_565_test seq_2046_train 0.99 0.99 100.0 99.30 9.66e-164
seq_108_test seq_3995_train 0.99 0.99 100.0 99.30 9.66e-164
seq_145_test seq_3072_train 0.99 0.99 100.0 99.30 9.66e-164
seq_251_test seq_3767_train 0.99 0.99 100.0 99.30 9.66e-164
seq_440_test seq_412_train 0.99 0.99 100.0 99.00 4.57e-163
seq_147_test seq_2290_train 1.00 1.00 96.3 96.30 9.20e-147
seq_24_test seq_3479_train 1.00 1.00 96.0 96.00 3.99e-145
seq_24_test seq_2428_train 1.00 1.00 96.0 96.00 3.99e-145
seq_507_test seq_4436_train 1.00 1.00 93.3 93.02 5.81e-131
seq_323_test seq_1361_train 1.00 1.00 92.3 92.02 7.18e-127
seq_323_test seq_3477_train 1.00 1.00 91.9 91.62 2.62e-125
seq_126_test seq_671_train 1.00 1.00 91.6 91.60 2.25e-124
seq_306_test seq_1835_train 1.00 0.98 91.7 90.14 4.60e-124