FusionInspector Outputs Described
The final output of FusionInspector is a file called 'finspector.FusionInspector.fusions.abridged.tsv', which you'll find in the --out_dir specified. The format of this file is tab-delimited and contains the following fields and formatting:
Scroll the window below to the right to see all the fields.
#FusionName JunctionReadCount SpanningFragCount LeftGene LeftLocalBreakpoint LeftBreakpoint RightGene RightLocalBreakpoint RightBreakpoint SpliceType LargeAnchorSupport NumCounterFusionLeft NumCounterFusionRight FAR_left FAR_right LeftBreakDinuc LeftBreakEntropy RightBreakDinuc RightBreakEntropy FFPM
THRA--AC090627.1 88 97 THRA^ENSG00000126351.8 11793 chr17:38243106:+ AC090627.1^ENSG00000235300.3 21568 chr17:46371709:+ ONLY_REF_SPLICE YES 24 0 7.44 186.00 GT 1.8892 AG 1.9656 8.6326
ACACA--STAC2 62 45 ACACA^ENSG00000132142.15 66695 chr17:35479453:- STAC2^ENSG00000141750.6 81161 chr17:37374426:- ONLY_REF_SPLICE YES 233 1 0.46 54.00 GT 1.9656 AG 1.9656 4.9929
RPS6KB1--SNF8 37 46 RPS6KB1^ENSG00000108443.9 1240 chr17:57970686:+ SNF8^ENSG00000159210.5 26089 chr17:47021337:- ONLY_REF_SPLICE YES 93 486 0.89 0.17 GT 1.3753 AG 1.8323 3.873
TOB1--SYNRG 22 35 TOB1^ENSG00000141232.4 2782 chr17:48943419:- SYNRG^ENSG00000006114.11 37847 chr17:35880751:- ONLY_REF_SPLICE YES 104 49 0.55 1.16 GT 1.4566 AG 1.8892 2.6598
VAPB--IKZF3 20 38 VAPB^ENSG00000124164.11 1396 chr20:56964573:+ IKZF3^ENSG00000161405.12 28254 chr17:37934020:- ONLY_REF_SPLICE YES 393 7 0.15 7.38 GT 1.9656 AG 1.7819 2.7064
THRA--AC090627.1 15 24 THRA^ENSG00000126351.8 11793 chr17:38243106:+ AC090627.1^ENSG00000235300.3 23800 chr17:46384693:+ ONLY_REF_SPLICE YES 24 153 1.60 0.26 GT 1.8892 AG 1.4295 1.8198
ZMYND8--CEP250 9 42 ZMYND8^ENSG00000101040.15 29057 chr20:45852970:- CEP250^ENSG00000126001.11 56963 chr20:34078463:+ ONLY_REF_SPLICE YES 64 6 0.80 7.43 GT 1.8295 AG 1.8062 2.3798
STX16--RAE1 9 29 STX16^ENSG00000124222.17 1816 chr20:57227143:+ RAE1^ENSG00000101146.8 18335 chr20:55929088:+ ONLY_REF_SPLICE YES 209 517 0.19 0.08 GT 1.9899 AG 1.9656 1.7732
MED1--STXBP4 12 14 MED1^ENSG00000125686.7 1249 chr17:37607291:- STXBP4^ENSG00000166263.9 44835 chr17:53218671:+ ONLY_REF_SPLICE YES 252 9 0.11 2.70 GT 1.3996 AG 1.7968 1.2132
AHCTF1--NAAA 7 28 AHCTF1^ENSG00000153207.10 1401 chr1:247094880:- NAAA^ENSG00000138744.10 50972 chr4:76846964:- ONLY_REF_SPLICE YES 24 52 1.44 0.68 GT 1.7232 AG 1.8062 1.6331
VAPB--IKZF3 3 44 VAPB^ENSG00000124164.11 1396 chr20:56964573:+ IKZF3^ENSG00000161405.12 26679 chr17:37944627:- ONLY_REF_SPLICE YES 393 0 0.12 48.00 GT 1.9656 AG 1.8892 2.1931
RAB22A--MYO9B 11 10 RAB22A^ENSG00000124209.3 2397 chr20:56886178:+ MYO9B^ENSG00000099331.9 23218 chr19:17256207:+ ONLY_REF_SPLICE YES 124 20 0.18 1.05 GT 1.6895 AG 1.9656 0.9799
MED1--ACSF2 11 9 MED1^ENSG00000125686.7 6915 chr17:37595418:- ACSF2^ENSG00000167107.8 36449 chr17:48548389:+ ONLY_REF_SPLICE YES 262 227 0.08 0.09 GT 1.9656 AG 1.9656 0.9333
RPS6KB1--SNF8 1 46 RPS6KB1^ENSG00000108443.9 1839 chr17:57971285:+ SNF8^ENSG00000159210.5 26089 chr17:47021337:- ONLY_REF_SPLICE NO 95 486 0.50 0.10 GT 1.9086 AG 1.8323 2.1932
STX16--RAE1 3 33 STX16^ENSG00000124222.17 3048 chr20:57234690:+ RAE1^ENSG00000101146.8 18335 chr20:55929088:+ ONLY_REF_SPLICE NO 195 517 0.19 0.07 GT 1.7465 AG 1.9656 1.6799
TIMM23--PARGP1 10 4 TIMM23^ENSG00000138297.9 6952 chr10:51606988:- PARGP1^ENSG00000214982.6 27883 chr10:51732772:+ ONLY_REF_SPLICE YES 131 0 0.11 15.00 GT 1.7819 AG 1.9086 0.6532
STX16--RAE1 2 33 STX16^ENSG00000124222.17 1867 chr20:57227194:+ RAE1^ENSG00000101146.8 18335 chr20:55929088:+ ONLY_REF_SPLICE YES 201 517 0.18 0.07 GT 1.9329 AG 1.9656 1.6332
SKA2--MYO19 7 8 SKA2^ENSG00000182628.8 1139 chr17:57232492:- MYO19^ENSG00000141140.12 29259 chr17:34863763:- ONLY_REF_SPLICE YES 170 68 0.09 0.23 GT 1.9086 AG 1.7819 0.6999
AHCTF1--NAAA 1 29 AHCTF1^ENSG00000153207.10 1850 chr1:247094431:- NAAA^ENSG00000138744.10 50972 chr4:76846964:- ONLY_REF_SPLICE NO 24 52 1.24 0.58 GT 1.9086 AG 1.8062 1.3999
SKA2--MYO19 6 6 SKA2^ENSG00000182628.8 1139 chr17:57232492:- MYO19^ENSG00000141140.12 29671 chr17:34863351:- ONLY_REF_SPLICE YES 170 98 0.08 0.13 GT 1.9086 AG 1.9086 0.56
STARD3--DOK5 6 6 STARD3^ENSG00000131748.11 1167 chr17:37793484:+ DOK5^ENSG00000101134.7 23084 chr20:53259997:+ ONLY_REF_SPLICE YES 511 0 0.03 13.00 GT 1.8892 AG 1.9656 0.56
VAPB--IKZF3 4 9 VAPB^ENSG00000124164.11 1396 chr20:56964573:+ IKZF3^ENSG00000161405.12 29371 chr17:37922746:- ONLY_REF_SPLICE YES 393 29 0.04 0.47 GT 1.9656 AG 1.9329 0.6066
DIDO1--TTI1 1 10 DIDO1^ENSG00000101191.12 1157 chr20:61569148:- TTI1^ENSG00000101407.8 31303 chr20:36642259:- ONLY_REF_SPLICE NO 17 24 0.67 0.48 GT 1.6402 AG 1.9329 0.5133
GLB1--CMTM7 2 6 GLB1^ENSG00000170266.11 23601 chr3:33055548:- CMTM7^ENSG00000153551.9 29734 chr3:32483332:+ ONLY_REF_SPLICE NO 15 0 0.56 9.00 GT 1.9329 AG 1.9086 0.3733
TRPC4AP--MRPL45 2 6 TRPC4AP^ENSG00000100991.7 2387 chr20:33665849:- MRPL45^ENSG00000174100.5 30682 chr17:36476502:+ ONLY_REF_SPLICE NO 362 553 0.02 0.02 GT 1.6895 AG 1.9656 0.3733
LAMP1--MCF2L 2 5 LAMP1^ENSG00000185896.9 1255 chr13:113951810:+ MCF2L^ENSG00000126217.16 46545 chr13:113718618:+ ONLY_REF_SPLICE YES 82 44 0.10 0.18 GT 1.5656 AG 1.9899 0.3266
CPNE1--PI3 2 4 CPNE1^ENSG00000214078.7 3826 chr20:34243124:- PI3^ENSG00000124102.4 14948 chr20:43804502:+ ONLY_REF_SPLICE NO 111 0 0.06 7.00 GT 1.6729 AG 1.9219 0.2799
ZMYND8--CEP250 2 4 ZMYND8^ENSG00000101040.15 29057 chr20:45852970:- CEP250^ENSG00000126001.11 57538 chr20:34079038:+ ONLY_REF_SPLICE NO 64 100 0.11 0.07 GT 1.8295 AG 1.8892 0.2799
DIDO1--TTI1 1 7 DIDO1^ENSG00000101191.12 1157 chr20:61569148:- TTI1^ENSG00000101407.8 34646 chr20:36634799:- ONLY_REF_SPLICE NO 17 25 0.50 0.35 GT 1.6402 AG 1.8892 0.3733
FITM2--UQCC1 2 3 FITM2^ENSG00000197296.5 1194 chr20:42939616:- UQCC1^ENSG00000101019.17 25551 chr20:33902568:- ONLY_REF_SPLICE YES 65 164 0.09 0.04 GT 1.8892 AG 1.8062 0.2333
ASTN2--RP11-281A20.1 2 2 ASTN2^ENSG00000148219.12 2762 chr9:120053605:- RP11-281A20.1^ENSG00000231901.1 38824 chr9:120632505:- ONLY_REF_SPLICE YES 2 0 1.67 5.00 GT 1.9219 AG 1.8892 0.1866
BRD4--RFX1 2 2 BRD4^ENSG00000141867.13 1256 chr19:15443101:- RFX1^ENSG00000132005.4 33748 chr19:14104707:- ONLY_REF_SPLICE NO 30 12 0.16 0.38 GT 1.9086 AG 0.9056 0.1866
TRPC4AP--MRPL45 2 2 TRPC4AP^ENSG00000100991.7 2387 chr20:33665849:- MRPL45^ENSG00000174100.5 31832 chr17:36478009:+ ONLY_REF_SPLICE YES 362 696 0.01 0.01 GT 1.6895 AG 1.9086 0.1866
BRD4--RFX1 2 1 BRD4^ENSG00000141867.13 1256 chr19:15443101:- RFX1^ENSG00000132005.4 35119 chr19:14094407:- ONLY_REF_SPLICE NO 30 34 0.13 0.11 GT 1.9086 AG 1.8295 0.14
CTD-2319I12.2--HEATR6 2 1 CTD-2319I12.2^ENSG00000267416.1 1164 chr17:58156833:+ HEATR6^ENSG00000068097.10 17130 chr17:58136882:- ONLY_REF_SPLICE NO 1 48 2.00 0.08 GT 1.8892 AG 1.8892 0.14
TRIM37--MYO19 2 1 TRIM37^ENSG00000108395.9 7217 chr17:57161363:- MYO19^ENSG00000141140.12 53005 chr17:34863351:- ONLY_REF_SPLICE NO 106 99 0.04 0.04 GT 1.7465 AG 1.9086 0.14
MED13--BCAS3 0 8 MED13^ENSG00000108510.5 37194 chr17:60023961:- BCAS3^ENSG00000141376.16 40195 chr17:58754814:+ NO_JUNCTION_READS_IDENTIFIED NO 0 0 9.00 9.00 TT 1.9329 GC 1.8062 0.3733
MED13--BCAS3 1 3 MED13^ENSG00000108510.5 3547 chr17:60129898:- BCAS3^ENSG00000141376.16 94861 chr17:59469338:+ ONLY_REF_SPLICE NO 16 54 0.29 0.09 GT 1.5546 AG 1.9086 0.1867
PIP4K2B--RAD51C 1 3 PIP4K2B^ENSG00000141720.7 9121 chr17:36933940:- RAD51C^ENSG00000108384.10 29822 chr17:56801401:+ ONLY_REF_SPLICE NO 441 69 0.01 0.07 GT 1.7968 AG 1.6402 0.1867
TRIM37--MYO19 1 3 TRIM37^ENSG00000108395.9 7217 chr17:57161363:- MYO19^ENSG00000141140.12 52593 chr17:34863763:- ONLY_REF_SPLICE NO 106 68 0.05 0.07 GT 1.7465 AG 1.7819 0.1867
BRD4--RFX1 1 2 BRD4^ENSG00000141867.13 1256 chr19:15443101:- RFX1^ENSG00000132005.4 32548 chr19:14109129:- ONLY_REF_SPLICE NO 30 2 0.13 1.33 GT 1.9086 AG 1.8892 0.14
PIP4K2B--RAD51C 1 1 PIP4K2B^ENSG00000141720.7 9121 chr17:36933940:- RAD51C^ENSG00000108384.10 31035 chr17:56809845:+ ONLY_REF_SPLICE NO 441 95 0.01 0.03 GT 1.7968 AG 1.9329 0.0934
PIP4K2B--RAD51C 1 1 PIP4K2B^ENSG00000141720.7 9121 chr17:36933940:- RAD51C^ENSG00000108384.10 31032 chr17:56809842:+ ONLY_REF_SPLICE NO 441 94 0.01 0.03 GT 1.7968 AG 1.9899 0.0934
PIP4K2B--RAD51C 1 1 PIP4K2B^ENSG00000141720.7 9121 chr17:36933940:- RAD51C^ENSG00000108384.10 32318 chr17:56811479:+ ONLY_REF_SPLICE NO 441 90 0.01 0.03 GT 1.7968 AG 1.9899 0.0934
The above results correspond to fusions in a breast cancer cell line BT474, first predicted by STAR-Fusion, and then further 'insilico validated' using FusionInspector.
There is also a .final file which contains most of the above fields along with the identity of the reads corresponding to fusion-supporting fragments. This file can be very large, and so the abridged version easier to navigate.
The columns of the output are described below:
#FusionName: name of the fusion as geneA--geneB
JunctionReadCount: number of split RNA-Seq reads that map and define the fusion breakpoint.
SpanningFragCount: number of paired-end reads that span the fusion breakpoint but the reads do not directly overlap the breakpoint.
LeftGene: identifier of the gene represented by the left section of the fusion transcript.
LeftLocalBreakpoint: position of the left fusion breakpoint in the context of the FusionInspector mini-fusion-gene contig.
LeftBreakpoint: position of the left fusion breakpoint in the context of the genome.
RightGene: identifier of the gene represented by the right section of the fusion transcript.
RightLocalBreakpoint: position of the right fusion breakpoint in the context of the FusionInspector min-fusion-gene contig.
RightBreakpoint: position of the right fusion breakpoint in the context of the genome.
SpliceType: category of support at the fusion breakpoint: {
ONLY_REF_SPLICE: fusion breakpoint occurs at reference (known) splice junctions.
INCL_NON_REF_SPLICE: fusion breakpoint occurs at a breakpoint that does not involve all reference (known) exon junctions.
NO_JUNCTION_READS_IDENTIFIED: only spanning fragments support the fusion. (can only happen if --min_junction_reads is set to zero).
}
LargeAnchorSupport: YES|NO, indicates whether there are at least 25 aligned bases on each side of the fusion breakpoint.
NumCounterFusionLeft: Number of RNA-Seq fragments supporting the alternative non-fused allele at the left junction breakpoint.
NumCounterFusionRight: Number of RNA-Seq fragments supporting the alternative non-fused allele at the right junction breakpoint.
FAR_left: Left fusion allelic ratio (see figure below)
FAR_right: Right fusion allelic ratio (see figure below)
LeftBreakDinuc: the genomic dinucleotides found at the left breakpoint (putative splice site if splicing is involved).
LeftBreakEntropy: entropy calculation for the 15 bases immediately upstream from the fusion junction.
RightBreakDinuc: the genomic dinucleotides found at the right breakpoint (putative splice site if splicing is involved).
RightBreakEntropy: entropy calculation for the 15 bases immediately downstream from the fusion junction.
FFPM: normalized measure of the quantity of RNA-Seq fragments supporting the fusion event as: fusion fragments per total million RNA-Seq fragments.
The fusion allelic ratio (FAR) is computed as a pragmatic way of estimating the relative expression of the fusion transcript as compared to the alternative non-fused allele of the gene. The method underlying the calculation is illustrated below:
In the above image, there are 2 fusion-supporting fragments (green), there are 3 fragments (blue) that correspond to the non-fused geneA allele, and there is 1 fragment (purple) supporting the non-fused geneB allele. The fusion allele ratio (FAR) is computed separately for each of the fused genes and reflects the proportion of evidence supporting the fused-allele as compared to the number of reads supporting the non-fused allele and overlapping the fusion transcript breakpoint. While this is not a highly accurate measurement of the ratio of fused vs. non-fused transcripts, it's a useful metric to serve as a proxy for this information. Accurate measurements would require performing abundance estimation based on knowing the exact structures and lengths of the full-length fused and non-fused isoforms being expressed. This additional functionality is still pending but will be addressed in a future software release.
For now, we use FFPM as our proxy for fusion transcript expression, and FAR as a proxy for relative expression of the fusion transcript to non-fused alleles.
Invoke the 'FusionInspector --include_Trinity' to include de novo reconstruction of fusion transcripts. See our De novo Reconstruction of Fusion Transcripts documentation for complete details.