findAlleles report
MiXCR generates a comprehensive summary of search for alleles process. Find alleles reports may be generated right along with findAlleles command using -r/--report for txt report and -j/--json-report for report in a json format, or can be exported using exportReports command.
Show sample report
======================================
Analysis date: Tue Oct 04 09:44:33 CEST 2022
Input file(s): current.clns
Output file(s): out/alleles_descrition.csv
Version: ; built=Tue Oct 04 09:44:19 CEST 2022; rev=411bb5fda4; lib=repseqio.v2.0
Command line arguments: findAlleles -f -t 1 -OsearchMutationsInCDR3=null --debugDir debug -j out/report.json -r out/report.txt --export-alleles-mutations out/alleles_descrition.csv current.clns
Analysis time: 7.95s
Clones score delta stats:
size: 31103
sum: 2332903.6998901367
min: -290.0
max: 348.0
avg: 75.00574542295395
quadratic mean: 104.13486938273368
std deviation: 72.23833436751467
Clones count with no change of score: 93048
Clones count with negative score change: 1124
Found alleles: 21
Zygotes: {1=41, 2=9}
Not enough information for allele search: [IGHJ2P*00, IGHV1-69D*00, IGHV3-65*00, IGHV4-28*00]
Genes with enough information for allele search: 40 (80%)
The same mutations in almost all clones, but not enough naive clones: {}
Possible additional allele, but not enough naive clones: {}
Found alleles that don't fit well to data: {}
======================================
{
"type": "findAllelesReport",
"commandLine": "findAlleles -f -t 1 --debugDir debug -j out/report.json --export-alleles-mutations out/alleles_descrition.csv current.clna",
"inputFiles": [
"current.clna"
],
"outputFiles": [
"out/alleles_descrition.csv"
],
"version": "; built=Tue Oct 04 15:17:35 CEST 2022; rev=ce6588ad8b; lib=repseqio.v2.0",
"searchHistoryForBCells": {
"IGHV1-58*00": {
"alleles": {
"addedKnownAllele": null,
"enrichedMutations": {},
"discardedEnrichedMutations": [],
"filteredOutByNaiveCount": [],
"result": [
"SA24G"
]
},
"clonesCount": 69,
"diversity": 27,
"enoughDiversity": true,
"differentMutationsCount": 35,
"mutationsWithEnoughDiversityCount": 1
},
"IGHJ4*00": {
"alleles": {
"addedKnownAllele": null,
"enrichedMutations": {},
"discardedEnrichedMutations": [],
"filteredOutByNaiveCount": [],
"result": [
""
]
},
"clonesCount": 11299,
"diversity": 620,
"enoughDiversity": true,
"differentMutationsCount": 48,
"mutationsWithEnoughDiversityCount": 0
},
"IGHV3-48*00": {
"alleles": {
"addedKnownAllele": null,
"enrichedMutations": {},
"discardedEnrichedMutations": [],
"filteredOutByNaiveCount": [],
"result": [
"SC17T,SA21G,SG22A,SC23A,SA87G,ST146C,SA187C,SG203T",
""
]
},
"clonesCount": 522,
"diversity": 83,
"enoughDiversity": true,
"differentMutationsCount": 158,
"mutationsWithEnoughDiversityCount": 22
}
},
"clonesCountWithNoChangeOfScore": 68999,
"clonesCountWithNegativeScoreChange": 3246,
"clonesScoreDeltaStats": {
"size": 59844,
"sum": 5723950.600250244,
"min": -377.0,
"max": 464.0,
"avg": 95.64786110972268,
"quadraticMean": 128.11717838119927,
"stdDeviation": 85.23860317260785
},
"foundAlleles": 20,
"zygotes": {
"1": 43,
"2": 6,
"3": 1
},
"allelesScoreChange": {
"IGHV1-58*00-M1-501828652": {
"size": 790,
"sum": 22272.0,
"min": -29.0,
"max": 29.0,
"avg": 28.19240506329114,
"quadraticMean": 29.0,
"stdDeviation": 6.80050270548995
},
"IGHJ4*00": {
"size": 0,
"sum": 0.0,
"min": "NaN",
"max": "NaN",
"avg": "NaN",
"quadraticMean": "NaN",
"stdDeviation": "NaN"
},
"IGHV3-48*00": {
"size": 0,
"sum": 0.0,
"min": "NaN",
"max": "NaN",
"avg": "NaN",
"quadraticMean": "NaN",
"stdDeviation": "NaN"
},
"IGHV3-48*00-M8-833988740": {
"size": 2185,
"sum": 341243.0,
"min": 29.0,
"max": 232.0,
"avg": 156.17528604118993,
"quadraticMean": 166.98923491249082,
"stdDeviation": 59.12938978989992
}
}
}
Clones score delta stats/clonesScoreDeltaStats- Stats of score change (V plus J) after aligning clone on built library.
Clones count with no change of score/clonesCountWithNoChangeOfScore- Clones count with no change of score (V plus J).
Clones count with negative score change/clonesCountWithNegativeScoreChange- How many clones align better on original library than on built one.
Found alleles/foundAlleles- Found alleles that weren't exist in original library.
Zygotes/zygotes- How many homozygous, heterozygous etc. Some genes are duplicated so 3 and 4 zygotes are not uncommon.
Not enough information for allele search- Genes that have not enough clones to determinate alleles.
Genes with enough information for allele search- How much genes had enough information to infer allele or it's absence.
The same mutations in almost all clones, but not enough naive clones- Alleles that have the same mutations in almost all clones, but there are not enough naive clones by complimentary gene with that mutation subset.
Possible additional allele, but not enough naive clones- May be there is one more allele, but there are not enough naive clones to be sure.
Found alleles that don't fit well to data- Alleles that make average clones scores worse.
searchHistoryForBCells- Info about process of allele search
allelesScoreChange- Stats of clones score change for every allele