The third file is
prefix.lima.summary, shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered.
ZMWs input (A) : 213120 ZMWs above all thresholds (B) : 176356 (83%) ZMWs below any threshold (C) : 36764 (17%) ZMW marginals for (C): Below min length : 26 (0%) Below min score : 0 (0%) Below min end score : 5138 (13%) Below min passes : 0 (0%) Below min score lead : 11656 (32%) Below min ref span : 3124 (8%) Without SMRTbell adapter : 25094 (68%) With bad adapter : 10349 (28%) <- Only with --bad-adapter-ratio Undesired hybrids : xxx (xx%) <- Only with --peek-guess Undesired same pairs : xxx (xx%) <- Only with --different Undesired diff pairs : xxx (xx%) <- Only with --same Undesired 5p--5p pairs : xxx (xx%) <- Only with --isoseq Undesired 3p--3p pairs : xxx (xx%) <- Only with --isoseq Undesired single side : xxx (xx%) <- Only with --isoseq Undesired no hit : xxx (xx%) <- Only with --isoseq ZMWs for (B): With same pair : 162244 (92%) With different pair : 14112 (8%) Coefficient of correlation : 32.79% ZMWs for (A): Allow diff pair : 157264 (74%) Allow same pair : 188026 (88%) Bad adapter yield loss : 10112 (5%) <- Only with --bad-adapter-ratio Bad adapter impurity : 10348 (5%) <- Only without --bad-adapter-ratio Reads for (B): Above length : 1278461 (100%) Below length : 2787 (0%)
Explanation of each block:
- Number of ZMWs that went into lima, how many ZMWs have been passed into the output file, and how many did not qualify.
- For those ZMWs that did not qualify, the marginal counts of each filter; each filter is explained in great detail elsewhere in this document.
- For those ZMWs that passed, how many have been flagged as having a same or different barcode pair. And what is the coefficient of variation for the barcode ZMW yield distribution in percent.
- For all input ZMWs, how many allow calling a same or different barcode pair. This a simplified version of, how many ZMWs have at least one full pass to allow a different barcode pair call and how many ZMWs have at least half an adapter, allowing a same barcode pair call.
- For those ZMWs that qualified, list the number of reads that are above and below the provided
--min-lengththreshold (details see here).