IDmut Report

IDmut Report: Fields

Name	Data Type
Sample	str
Branches	dict[str, str]
Reference	str
Discard reads with mapping qualities below this threshold	int
Specify the Phred score encoding of FASTQ and SAM/BAM/CRAM files	int
Mark base calls with Phred scores lower than this threshold as ambiguous	int
Mark each insertion on the base to its 3’ (True) or 5’ (False) side	bool
Mark all ambiguous insertions and deletions (indels)	bool
Retain the overhangs of paired-end mates that dovetail	bool
Clip this many bases from the 5’ end of each read	int
Clip this many bases from the 3’ end of each read	int
Discard alignment maps with fewer than this many reads	int
Number of reads in SAM/BAM/CRAM file	int
Number of reads processed successfully	int
Number of batches	int
Checksums of batches (SHA-512)	dict[str, list[str]]
Checksum of reference sequence (SHA-512)	str
Time began	str
Time ended	str
Time taken (minutes)	float
Version of SEISMIC-RNA	str

IDmut Report: Example

{
    "Sample": "sample1",
    "Branches": {
        "align": "",
        "idmut": ""
    },
    "Reference": "myref",
    "Discard reads with mapping qualities below this threshold": 25,
    "Specify the Phred score encoding of FASTQ and SAM/BAM/CRAM files": 33,
    "Mark base calls with Phred scores lower than this threshold as ambiguous": 25,
    "Mark each insertion on the base to its 3' (True) or 5' (False) side": true,
    "Mark all ambiguous insertions and deletions (indels)": true,
    "Retain the overhangs of paired-end mates that dovetail": true,
    "Clip this many bases from the 5' end of each read": 4,
    "Clip this many bases from the 3' end of each read": 4,
    "Discard alignment maps with fewer than this many reads": 1000,
    "Number of reads in SAM/BAM/CRAM file": 3595,
    "Number of reads processed successfully": 3595,
    "Number of batches": 1,
    "Checksums of batches (SHA-512)": {
        "idmut": [
            "8726f5b45a8588b5d462e47be651f232343214f7f755d816f6a2803e3b6bbdf17bb808ab86a74444ca2c6fcb7ef8a97f14482824b6aa524747f23fe73ab18635"
        ]
    },
    "Checksum of reference sequence (SHA-512)": "0686c09f78bae859b81f5527501018fe9768ef7595cbe1ed966aa549e227daeef8a85bf3a3dd01b9d487286fcf319e0c71ee25516d3d16b10acfe72e6eb7bcd7",
    "Time began": "2026-05-31 at 12:53:11",
    "Time ended": "2026-05-31 at 12:53:12",
    "Time taken (minutes)": 0.01,
    "Version of SEISMIC-RNA": "0.25.3"
}