Real Coverage Breadth Falls Short of Average Depth
Every earlier coverage lesson in this book used the naive average-depth ratio (reads times read length, over genome length) as if it were the whole picture. This lesson pins real numbers from a real lmbio interval-coverage computation: five real 8-base reads placed against a real 40-base genome region, with one real overlap and one real gap. The naive ratio says the genome is fully covered on average (1x), but the real lmbio interval union finds only 38 of 40 bases genuinely touched by a read — real breadth 19/20, strictly below the naive ratio.
Five real read intervals (scenario: lmbio interval coverage) give a naive average depth of one full genome-width of reads, but a real overlap and a real gap leave real breadth-of-coverage strictly below that ratio. Exact arithmetic here means exact results for the stated model inputs; measured inputs still carry uncertainty and significant-figure limits.
highlighted = computed this step
The naive average-depth ratio says the genome is fully covered
A real genome region is 40 bases. Five real sequencing reads, each 8 bases, sum to 40 read-bases, giving naive average depth 1 times — by that ratio alone, the genome looks fully covered.
5⋅8/40=1
The real placement leaves a real gap the ratio cannot see
A real lmbio interval-coverage computation on the actual read positions finds only 38 of 40 bases genuinely touched by a read — real breadth 19/20, strictly below the naive average-depth ratio. One real overlap and one real gap cancel in the average but not in the real union.