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 H3K27ac_test.csv.gz against train set H3K27ac_train.csv.gz
Data Leakage:!WarningHow a flag is decided →
gb-qc v1.0.0 · run 2026-09-15 22:31:11

Basic Descriptive Statistics

Filename H3K27ac_test.csv.gz H3K27ac_train.csv.gz
Number of sequences 1616 30000
Minimum length 1000 1000
Mean length 1000.00 1000.00
Maximum length 1000 1000
!

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 H3K27ac_test.csv.gz H3K27ac_train.csv.gz
Data Leakage (percentage) 0.56% 0.05%
Data Leakage (count) 9 16
Similarity Histogram
19 high-similarity alignments
Query (Q) Target (T) Q Cov. T Cov. % Identity % Similarity E-value Alignment
seq_1020_test seq_17345_train 1.00 1.00 96.5 96.11 0.00e+00
seq_1216_test seq_5642_train 0.98 0.98 97.8 95.94 0.00e+00
seq_1216_test seq_2391_train 0.99 0.99 96.1 95.33 0.00e+00
seq_1216_test seq_21519_train 0.98 0.98 96.8 94.48 0.00e+00
seq_875_test seq_5055_train 0.99 1.00 93.8 93.24 0.00e+00
seq_1216_test seq_20510_train 0.95 0.95 97.4 92.92 0.00e+00
seq_1213_test seq_2396_train 0.95 0.95 97.6 92.33 0.00e+00
seq_865_test seq_29313_train 0.97 0.97 94.7 92.24 0.00e+00
seq_1301_test seq_5434_train 0.96 0.96 96.0 92.16 0.00e+00
seq_857_test seq_13055_train 0.99 0.99 93.0 91.79 0.00e+00
seq_875_test seq_11388_train 0.99 0.99 92.3 91.01 0.00e+00
seq_1263_test seq_8157_train 0.99 1.00 91.5 90.86 0.00e+00
seq_1020_test seq_14884_train 0.94 0.94 96.5 90.81 0.00e+00
seq_865_test seq_9495_train 0.96 0.96 94.7 90.72 0.00e+00
seq_1301_test seq_14884_train 0.94 0.94 96.5 90.61 0.00e+00
seq_857_test seq_16868_train 0.97 0.97 93.0 90.21 0.00e+00
seq_1388_test seq_10369_train 0.99 0.99 90.8 90.16 0.00e+00
seq_875_test seq_13055_train 0.95 0.96 95.2 90.06 0.00e+00
seq_857_test seq_5055_train 0.96 0.96 93.8 90.05 0.00e+00