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"
}