Filter Report ------------- Filter Report: Fields ^^^^^^^^^^^^^^^^^^^^^ ================================================================================================================================ ==================== Name Data Type ================================================================================================================================ ==================== Sample str Branches dict[str, str] Reference str Region str Region 5' end int Region 3' end int Use the default options for this chemical probe str Count as mutations list[str] Count as matches list[str] Mask positions with base A bool Mask positions with base C bool Mask positions with base G bool Mask positions with base U bool Mask stretches of at least this many consecutive A bases (0 disables); defaults to 5 for chemical probes, 0 for none int Mask additional positions from a list list[int] Mask positions with fewer than this many informative base calls int Mask positions with more than this fraction of mutated base calls float Drop reads with fewer than this many bases covering the region int Drop reads covering less than this fraction of the region float Drop paired-end reads with discontiguous mates bool Drop reads with less than this fraction of informative base calls float Drop reads with more than this fraction of mutated base calls float Filter out mutations separated by fewer than this many bases int If two mutations are closer than --min-mut-gap positions, MERGE the mutations, DROP the read, or AUTO-select based on the probe. str Stop the filter step after this many iterations (0 for no limit) int Correct observer bias using a quick (typically linear time) heuristic bool Treat mutated fractions under this threshold as 0 with --quick-unbias float Total number of positions in the region int Number of positions masked for having base A int Number of positions masked for having base C int Number of positions masked for having base G int Number of positions masked for having base U int Number of positions masked for having base N int Number of positions in stretches of consecutive A bases int Number of positions masked from a list int Number of positions with too few informative base calls int Number of positions with too many mutations int Number of positions kept after filtering int Positions masked for having base A list[int] Positions masked for having base C list[int] Positions masked for having base G list[int] Positions masked for having base U list[int] Positions masked for having base N list[int] Positions in stretches of consecutive A bases list[int] Positions masked from a list list[int] Positions with too few informative base calls list[int] Positions with too many mutations list[int] Positions kept after filtering list[int] Total number of reads before filtering int Number of reads dropped from a list int Number of reads dropped due to too few bases covering the region int Number of reads dropped due to covering too small a fraction of the region int Number of reads dropped due to discontiguous mates int Number of reads dropped due to too few informative base calls int Number of reads dropped due to too many mutations int Number of reads dropped due to two mutations too close int Number of reads kept after filtering int Number of iterations until convergence (0 if not converged) int Number of batches int Checksums of batches (SHA-512) dict[str, list[str]] Time began str Time ended str Time taken (minutes) float Version of SEISMIC-RNA str ================================================================================================================================ ==================== Filter Report: Example ^^^^^^^^^^^^^^^^^^^^^^ :: { "Sample": "sample1", "Branches": { "align": "", "idmut": "", "filter": "" }, "Reference": "myref", "Region": "full", "Region 5' end": 1, "Region 3' end": 80, "Use the default options for this chemical probe": "DMS", "Count as mutations": [ "A -> C", "A -> D", "A -> G", "A -> I", "A -> T", "C -> A", "C -> D", "C -> G", "C -> I", "C -> T", "G -> A", "G -> C", "G -> D", "G -> I", "G -> T", "N -> D", "N -> I", "T -> A", "T -> C", "T -> D", "T -> G", "T -> I" ], "Count as matches": [ "A -> A", "C -> C", "G -> G", "T -> T" ], "Mask positions with base A": false, "Mask positions with base C": false, "Mask positions with base G": true, "Mask positions with base U": true, "Mask stretches of at least this many consecutive A bases (0 disables); defaults to 5 for chemical probes, 0 for none": 5, "Mask additional positions from a list": [], "Mask positions with fewer than this many informative base calls": 1000, "Mask positions with more than this fraction of mutated base calls": 1.0, "Drop reads with fewer than this many bases covering the region": 1, "Drop reads covering less than this fraction of the region": 0.0, "Drop paired-end reads with discontiguous mates": true, "Drop reads with less than this fraction of informative base calls": 0.95, "Drop reads with more than this fraction of mutated base calls": 1.0, "Filter out mutations separated by fewer than this many bases": 4, "If two mutations are closer than --min-mut-gap positions, MERGE the mutations, DROP the read, or AUTO-select based on the probe.": "drop", "Stop the filter step after this many iterations (0 for no limit)": 0, "Correct observer bias using a quick (typically linear time) heuristic": true, "Treat mutated fractions under this threshold as 0 with --quick-unbias": 0.001, "Total number of positions in the region": 80, "Number of positions masked for having base A": 0, "Number of positions masked for having base C": 0, "Number of positions masked for having base G": 13, "Number of positions masked for having base U": 22, "Number of positions masked for having base N": 0, "Number of positions in stretches of consecutive A bases": 5, "Number of positions masked from a list": 0, "Number of positions with too few informative base calls": 14, "Number of positions with too many mutations": 0, "Number of positions kept after filtering": 26, "Positions masked for having base A": [], "Positions masked for having base C": [], "Positions masked for having base G": [ 1, 6, 7, 14, 31, 33, 34, 35, 39, 47, 49, 60, 69 ], "Positions masked for having base U": [ 13, 15, 18, 22, 25, 26, 27, 30, 41, 46, 51, 52, 53, 54, 58, 61, 62, 64, 67, 71, 76, 79 ], "Positions masked for having base N": [], "Positions in stretches of consecutive A bases": [ 8, 9, 10, 11, 12 ], "Positions masked from a list": [], "Positions with too few informative base calls": [ 2, 3, 4, 5, 66, 68, 70, 72, 73, 74, 75, 77, 78, 80 ], "Positions with too many mutations": [], "Positions kept after filtering": [ 16, 17, 19, 20, 21, 23, 24, 28, 29, 32, 36, 37, 38, 40, 42, 43, 44, 45, 48, 50, 55, 56, 57, 59, 63, 65 ], "Total number of reads before filtering": 3595, "Number of reads dropped from a list": 0, "Number of reads dropped due to too few bases covering the region": 0, "Number of reads dropped due to covering too small a fraction of the region": 0, "Number of reads dropped due to discontiguous mates": 0, "Number of reads dropped due to too few informative base calls": 134, "Number of reads dropped due to too many mutations": 0, "Number of reads dropped due to two mutations too close": 16, "Number of reads kept after filtering": 3445, "Number of iterations until convergence (0 if not converged)": 2, "Number of batches": 1, "Checksums of batches (SHA-512)": { "filter": [ "bcfd01c9340c63d1474e58e72657e845a6a0681988a68aaf205b30d2003e781ee492327f1ea6f44637853309ce323d4714b0458ed3915ddca1ec951751d4c3e6" ] }, "Time began": "2026-05-31 at 12:53:14", "Time ended": "2026-05-31 at 12:53:26", "Time taken (minutes)": 0.2, "Version of SEISMIC-RNA": "0.25.3" }