Mask Report

Mask Report: Fields

Name	Data Type
Name of Sample	str
Name of Reference	str
Name of Region	str
5’ end of Region	int
3’ end of Region	int
Count the Following as Mutations	list[str]
Count the Following as Matches	list[str]
Exclude G/U Bases	bool
Exclude Poly(A) Sequences of at Least This Length (nt)	int
Exclude User-Defined Positions	list[int]
Minimum Number of Informative Reads per Position	int
Maximum Fraction of Mutations per Position	float
Number of Positions Initially Given	int
Number of Positions Cut – G/U Base	int
Number of Positions Cut – Poly(A) Sequence	int
Number of Positions Cut – User-Specified	int
Number of Positions Cut – Too Few Informative Reads	int
Number of Positions Cut – Too Many Mutations	int
Number of Positions Ultimately Kept	int
Positions Cut – G/U Base	list[int]
Positions Cut – Poly(A) Sequence	list[int]
Positions Cut – User-Specified	list[int]
Positions Cut – Too Few Informative Reads	list[int]
Positions Cut – Too Many Mutations	list[int]
Positions Ultimately Kept	list[int]
Minimum Fraction of Informative Positions per Read	float
Maximum Fraction of Mutations per Read	float
Minimum Gap Between Mutations (nt)	int
Number of Reads Initially Given	int
Number of Reads Cut – Too Few Informative Positions	int
Number of Reads Cut – Too Many Mutations	int
Number of Reads Cut – Mutations Too Close Together	int
Number of Reads Ultimately Kept	int
Number of Batches	int
MD5 Checksums of Batches	dict[str, list[str]]
Branches	list[str]
Time Began	str
Time Ended	str
Time Taken (minutes)	float
Version of SEISMIC-RNA	str

Mask Report: Example

{
    "Name of Sample": "ldi",
    "Name of Reference": "sars2_1799",
    "Name of Region": "fse",
    "5' end of Region": 397,
    "3' end of Region": 426,
    "Count the Following as Mutations": [
        "A -> C",
        "A -> G",
        "A -> T",
        "C -> A",
        "C -> G",
        "C -> T",
        "G -> A",
        "G -> C",
        "G -> T",
        "T -> A",
        "T -> C",
        "T -> G"
    ],
    "Count the Following as Matches": [
        "A -> A",
        "C -> C",
        "G -> G",
        "T -> T"
    ],
    "Exclude G/U Bases": true,
    "Exclude Poly(A) Sequences of at Least This Length (nt)": 5,
    "Exclude User-Defined Positions": [],
    "Minimum Number of Informative Reads per Position": 1000,
    "Maximum Fraction of Mutations per Position": 0.5,
    "Number of Positions Initially Given": 30,
    "Number of Positions Cut -- G/U Base": 15,
    "Number of Positions Cut -- Poly(A) Sequence": 5,
    "Number of Positions Cut -- User-Specified": 0,
    "Number of Positions Cut -- Too Few Informative Reads": 0,
    "Number of Positions Cut -- Too Many Mutations": 0,
    "Number of Positions Ultimately Kept": 10,
    "Positions Cut -- G/U Base": [
        398,
        399,
        400,
        401,
        402,
        403,
        404,
        405,
        407,
        411,
        412,
        415,
        422,
        425,
        426
    ],
    "Positions Cut -- Poly(A) Sequence": [
        416,
        417,
        418,
        419,
        420
    ],
    "Positions Cut -- User-Specified": [],
    "Positions Cut -- Too Few Informative Reads": [],
    "Positions Cut -- Too Many Mutations": [],
    "Positions Ultimately Kept": [
        397,
        406,
        408,
        409,
        410,
        413,
        414,
        421,
        423,
        424
    ],
    "Minimum Fraction of Informative Positions per Read": 0.0,
    "Maximum Fraction of Mutations per Read": 0.1,
    "Minimum Gap Between Mutations (nt)": 0,
    "Number of Reads Initially Given": 562325,
    "Number of Reads Cut -- Too Few Informative Positions": 0,
    "Number of Reads Cut -- Too Many Mutations": 289974,
    "Number of Reads Cut -- Mutations Too Close Together": 0,
    "Number of Reads Ultimately Kept": 272351,
    "Number of Batches": 16,
    "MD5 Checksums of Batches": {
        "mask": [
            "d295b42cc757255ad29070f00fb6a51d",
            "9f8d6ba42947fb1ee3b9a0b67879e99e",
            "194824b402bced072049a46d8c7effb6",
            "b723dc6f19f93bca0827155cca36965d",
            "dfc527236af3a5888d3753b2c0041dc3",
            "27eb008e907d48d932626098f4587178",
            "c2c0ee505c970d55d2e17e8a2d8ba48c",
            "42babd92a5ffdd13e29441f034a6b167",
            "901b083617e6a66df5a68dc03323b791",
            "a13183811fadb0a9906d71a729aee04d",
            "bc18c08eca71f48d57e0119392042cc3",
            "1680be76740c49f0c216574ca61f3ed4",
            "beebe1e830d72da7296aeb62a29e057b",
            "81f2ed98056df9611354e0aa3a219971",
            "09c4d2b19c4c720bd24b2f432b908cb9",
            "c5cec619b953ff80609f172a04abf6ec"
        ]
    },
    "Branches": [],
    "Time Began": "2023-12-18 at 17:51:53",
    "Time Ended": "2023-12-18 at 17:52:09",
    "Time Taken (minutes)": 0.26,
    "Version of SEISMIC-RNA": "0.10.0"
}