Synthetic BAM group-summary test (CC0-1.0)
Use reference.gff3 under Route 3, choose sequencing depth, fixed 100-bp windows and Average.
Upload all four group-*.bam files and all four matching .bam.bai files.
Without metadata grouping, expect one multi-line/multi-area series per sample (four).
To group, upload bam-groups.csv, choose Summarize samples by group, group column condition, and Mean.
Expect Control and Treatment series. You can instead choose batch to compare Batch 1 and Batch 2.
For chr1:101-200, Control mean=(20/15+20/12)/2=1.5. Treatment has one sample at 2.5 and one absent window; exclude-missing gives 2.5, zero-missing gives 1.25.
This is an unweighted mean of the per-sample window values, not pooled read depth. See bam-groups-expected.json for sample checkpoints.
