Parameters
input_file: 20090724_LUd4_8_hg19_ensembl59_S_iCLIP_TIAL1_HeLa_bedGraph-cDNA.bed.gz
input_res_type: single hits (=G+T), cDNA counts
mapped_to: hg19
annot_ver: ensembl59
maxU_within: -300
maxD_within: 300
maxU_flanking: -1000
maxD_flanking: 1000
smoothing: 0

Distribution of x-link sites and counts in RNAmaps.
[x-link sites] total: 17357
[x-link sites] used in any map: 5688 (32.77%)
[single hits (=G+T), cDNA counts] total: 17357
[single hits (=G+T), cDNA counts] used in any map: 6025 (32.74%)

map	span (upstream; downstream)	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map
exon-intron	-300; 300	1453	8.37%	25.55%	1498	8.14%	24.86%
intron-exon	-300; 300	1129	6.50%	19.85%	1161	6.31%	19.27%
5-ncRNA	-1000; 300	363	2.09%	6.38%	423	2.30%	7.02%
ncRNA-3	-300; 1000	513	2.96%	9.02%	575	3.12%	9.54%
ORF-3UTR	-300; 300	900	5.19%	15.82%	951	5.17%	15.78%
5UTR-ORF	-300; 300	30	0.17%	0.53%	31	0.17%	0.51%
inter-5UTR	-1000; 300	78	0.45%	1.37%	80	0.43%	1.33%
3UTR-inter	-300; 1000	1018	5.87%	17.90%	1073	5.83%	17.81%
inter-5	-1000; 300	295	1.70%	5.19%	308	1.67%	5.11%
3-inter	-300; 1000	1476	8.50%	25.95%	1611	8.75%	26.74%
BP best in intron	-300; 100	597	3.44%	10.50%	609	3.31%	10.11%

Download statistics in tab-delimited format.
Download graphs in tab-delimited format.

RNAmap exon-intron

junction is at position zero.
upstream is regions of type: ORF, 3UTR, 5UTR
downstream is regions of type: intron

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	1402	8.08%	24.65%	96.49%	1306	1.0416
anti	51	0.29%	0.90%	3.51%	40	0.03789
both	1453	8.37%	25.55%	100.00%	1346	1.07949
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	1443	7.84%	23.95%	96.33%	1306	1.07207
anti	55	0.30%	0.91%	3.67%	40	0.0408618
both	1498	8.14%	24.86%	100.00%	1346	1.11293

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr1:45976739@+	-281; 300	MMACHC	0; 9	0; 9
chr2:198284903@-	-98; 300	SF3B1	6; 0	7; 0
chr1:186330752@-	-44; 300	TPR	4; 0	4; 0
chrX:151129695@-	-71; 300	GABRE	3; 0	3; 0
chr8:62596596@-	-75; 300	ASPH	3; 0	4; 0
chr7:128411528@+	-300; 107	CALU	3; 0	3; 0
chr5:39021139@-	-49; 300	RICTOR	3; 0	3; 0
chr3:41281934@+	-300; 300	CTNNB1	3; 0	3; 0
chr2:228207535@+	-38; 300	MFF	3; 0	3; 0
chr18:43595867@-	-162; 300	PSTPIP2	3; 0	3; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr1:45976739@+	-281; 300	MMACHC	0; 9	0; 9
chr2:198284903@-	-98; 300	SF3B1	6; 0	7; 0
chr8:62596596@-	-75; 300	ASPH	3; 0	4; 0
chr12:50158717@+	-300; 300	TMBIM6	3; 0	4; 0
chr1:186330752@-	-44; 300	TPR	4; 0	4; 0
chrX:151129695@-	-71; 300	GABRE	3; 0	3; 0
chr7:72858312@-	-73; 300	BAZ1B	1; 0	3; 0
chr7:128411528@+	-300; 107	CALU	3; 0	3; 0
chr5:114878645@-	-272; 300	FEM1C	2; 0	3; 0
chr5:39021139@-	-49; 300	RICTOR	3; 0	3; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap intron-exon

junction is at position zero.
upstream is regions of type: intron
downstream is regions of type: ORF, 3UTR, 5UTR

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	1074	6.19%	18.88%	95.13%	970	1.05191
anti	55	0.32%	0.97%	4.87%	51	0.0538688
both	1129	6.50%	19.85%	100.00%	1021	1.10578
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	1106	6.01%	18.36%	95.26%	970	1.08325
anti	55	0.30%	0.91%	4.74%	51	0.0538688
both	1161	6.31%	19.27%	100.00%	1021	1.13712

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr9:131456919@+	-292; 300	SET	13; 0	16; 0
chr5:179041959@-	-293; 300	HNRNPH1	9; 0	10; 0
chr10:112657785@+	-300; 300	PDCD4	9; 0	12; 0
chr4:41699176@+	-300; 300	LIMCH1	7; 0	10; 0
chr15:45009804@+	-300; 277	B2M	6; 0	7; 0
chr8:128753204@+	-241; 235	MYC	4; 0	4; 0
chr5:32711539@+	-300; 171	NPR3	4; 0	4; 0
chr15:69072480@-	-134; 300	ANP32A	4; 0	4; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	3; 0	3; 0
chr20:34327468@-	-276; 222	RBM39	3; 0	3; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr9:131456919@+	-292; 300	SET	13; 0	16; 0
chr10:112657785@+	-300; 300	PDCD4	9; 0	12; 0
chr5:179041959@-	-293; 300	HNRNPH1	9; 0	10; 0
chr4:41699176@+	-300; 300	LIMCH1	7; 0	10; 0
chr15:45009804@+	-300; 277	B2M	6; 0	7; 0
chr12:54678332@+	-116; 300	HNRNPA1	3; 0	5; 0
chr8:128753204@+	-241; 235	MYC	4; 0	4; 0
chr5:32711539@+	-300; 171	NPR3	4; 0	4; 0
chr15:69072480@-	-134; 300	ANP32A	4; 0	4; 0
chr7:26230747@-	-300; 68	HNRNPA2B1	3; 0	3; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 5-ncRNA

junction is at position zero.
upstream is regions of type: intron, inter, telo
downstream is regions of type: ncRNA

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	199	1.15%	3.50%	54.82%	99	0.917051
anti	164	0.94%	2.88%	45.18%	119	0.75576
both	363	2.09%	6.38%	100.00%	217	1.67281
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	237	1.29%	3.93%	56.03%	99	1.09217
anti	186	1.01%	3.09%	43.97%	119	0.857143
both	423	2.30%	7.02%	100.00%	217	1.94931

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65269806@+	-1000; 29	MALAT1	62; 0	91; 0
chrUn_gl000220:109077@+	-758; 300	18S	9; 0	9; 0
chr8:128231332@-	-1000; 139	AC020688.1	7; 0	7; 0
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 6	0; 6
chr17:57918626@+	-338; 36	hsa-mir-21	6; 0	6; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	6; 0	9; 0
chr4:30795591@-	-1000; 24	RP11-619J20.1	0; 5	0; 5
chr7:4811073@-	-1000; 300	AC092610.1	0; 4	0; 5
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 4	0; 4
chr3:49571651@-	-1000; 300	AC104452.1	0; 4	0; 4

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65269806@+	-1000; 29	MALAT1	62; 0	91; 0
chr6:71444374@+	-1000; 146	RP11-160A9.2, SMAP1	0; 3	0; 19
chrUn_gl000220:109077@+	-758; 300	18S	9; 0	9; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	6; 0	9; 0
chr8:128231332@-	-1000; 139	AC020688.1	7; 0	7; 0
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 6	0; 6
chr17:57918626@+	-338; 36	hsa-mir-21	6; 0	6; 0
chr14:74055600@-	-1000; 36	AC005225.1	2; 0	6; 0
chr7:4811073@-	-1000; 300	AC092610.1	0; 4	0; 5
chr4:30795591@-	-1000; 24	RP11-619J20.1	0; 5	0; 5

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap ncRNA-3

junction is at position zero.
upstream is regions of type: ncRNA
downstream is regions of type: intron, inter, telo

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	401	2.31%	7.05%	78.17%	224	1.30619
anti	112	0.65%	1.97%	21.83%	83	0.364821
both	513	2.96%	9.02%	100.00%	307	1.67101
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	458	2.49%	7.60%	79.65%	224	1.49186
anti	117	0.64%	1.94%	20.35%	83	0.381107
both	575	3.12%	9.54%	100.00%	307	1.87296

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	97; 0	126; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 9	0; 12
chrUn_gl000220:118417@+	-300; 1000	28S	8; 0	10; 0
chrUn_gl000220:110946@+	-300; 539	18S	6; 0	7; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	6; 0	8; 0
chr9:74622795@-	-128; 1000	RP11-346E17.4	4; 0	4; 0
chr7:44507903@+	-204; 1000	AC004453.8	4; 0	4; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	4; 0	4; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 4	0; 5
chr2:191798136@-	-300; 1000	AC067945.1	0; 4	0; 4

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	97; 0	126; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 9	0; 12
chrUn_gl000220:118417@+	-300; 1000	28S	8; 0	10; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	6; 0	8; 0
chrUn_gl000220:110946@+	-300; 539	18S	6; 0	7; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 4	0; 5
chr14:74055527@-	-37; 1000	AC005225.1	2; 0	5; 0
chr1:171639418@-	-194; 1000	RP4-560B9.2	2; 0	5; 0
chr9:74622795@-	-128; 1000	RP11-346E17.4	4; 0	4; 0
chr9:12972840@-	-298; 1000	RP11-382H24.3	3; 0	4; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap ORF-3UTR

junction is at position zero.
upstream is regions of type: ORF
downstream is regions of type: 3UTR

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	888	5.12%	15.61%	98.67%	572	1.52055
anti	12	0.07%	0.21%	1.33%	12	0.0205479
both	900	5.19%	15.82%	100.00%	584	1.5411
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	939	5.10%	15.59%	98.74%	572	1.60788
anti	12	0.07%	0.20%	1.26%	12	0.0205479
both	951	5.17%	15.78%	100.00%	584	1.62842

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr19:13054727@+	-101; 288	CALR	16; 0	18; 0
chrX:70520705@+	-300; 156	NONO	11; 0	12; 0
chr3:149087560@-	-53; 300	TM4SF1	9; 0	9; 0
chr1:35650053@-	-70; 300	SFPQ	8; 0	8; 0
chr7:128409221@+	-53; 300	CALU	7; 0	7; 0
chr21:44836618@-	-189; 300	SIK1	7; 0	7; 0
chr14:62213803@+	-76; 300	HIF1A	7; 0	8; 0
chr1:54497690@-	-144; 172	TMEM59	7; 0	7; 0
chr7:148700882@-	-209; 300	PDIA4	6; 0	6; 0
chr22:38881684@-	-300; 300	DDX17	6; 0	6; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr19:13054727@+	-101; 288	CALR	16; 0	18; 0
chrX:70520705@+	-300; 156	NONO	11; 0	12; 0
chr3:149087560@-	-53; 300	TM4SF1	9; 0	9; 0
chr2:189876774@+	-211; 300	COL3A1	6; 0	8; 0
chr14:62213803@+	-76; 300	HIF1A	7; 0	8; 0
chr14:50360982@+	-264; 254	ARF6	5; 0	8; 0
chr1:35650053@-	-70; 300	SFPQ	8; 0	8; 0
chr1:207533847@+	-300; 231	CD55	6; 0	8; 0
chr7:128409221@+	-53; 300	CALU	7; 0	7; 0
chr5:122359566@-	-66; 300	PPIC	4; 0	7; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 5UTR-ORF

junction is at position zero.
upstream is regions of type: 5UTR
downstream is regions of type: ORF

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	24	0.14%	0.42%	80.00%	23	0.857143
anti	6	0.03%	0.11%	20.00%	5	0.214286
both	30	0.17%	0.53%	100.00%	28	1.07143
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	24	0.13%	0.40%	77.42%	23	0.857143
anti	7	0.04%	0.12%	22.58%	5	0.25
both	31	0.17%	0.51%	100.00%	28	1.10714

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr7:112424879@-	-64; 300	TMEM168	2; 0	2; 0
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 2	0; 2
chrX:47082893@+	-300; 132	PCTK1	1; 0	1; 0
chr9:114937514@-	-87; 51	SUSD1	1; 0	1; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 1	0; 1
chr6:31508971@-	-66; 265	BAT1	1; 0	1; 0
chr6:166401613@+	-250; 300	AL132661.1	0; 1	0; 1
chr6:43139364@+	-223; 271	SRF	1; 0	1; 0
chr6:33168574@+	-177; 300	SLC39A7	1; 0	1; 0
chr5:34915781@+	-151; 110	BRIX1	0; 1	0; 2

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr7:112424879@-	-64; 300	TMEM168	2; 0	2; 0
chr5:34915781@+	-151; 110	BRIX1	0; 1	0; 2
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 2	0; 2
chrX:47082893@+	-300; 132	PCTK1	1; 0	1; 0
chr9:114937514@-	-87; 51	SUSD1	1; 0	1; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 1	0; 1
chr6:31508971@-	-66; 265	BAT1	1; 0	1; 0
chr6:166401613@+	-250; 300	AL132661.1	0; 1	0; 1
chr6:43139364@+	-223; 271	SRF	1; 0	1; 0
chr6:33168574@+	-177; 300	SLC39A7	1; 0	1; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap inter-5UTR

junction is at position zero.
upstream is regions of type: inter, telo
downstream is regions of type: 5UTR

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	26	0.15%	0.46%	33.33%	23	0.38806
anti	52	0.30%	0.91%	66.67%	44	0.776119
both	78	0.45%	1.37%	100.00%	67	1.16418
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	27	0.15%	0.45%	33.75%	23	0.402985
anti	53	0.29%	0.88%	66.25%	44	0.791045
both	80	0.43%	1.33%	100.00%	67	1.19403

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr6:166401114@+	-1000; 249	AL132661.1	0; 4	0; 4
chr17:7387865@+	-741; 109	POLR2A	3; 0	3; 0
chr12:54673914@-	-1000; 62	CBX5	0; 3	0; 3
chr8:101734314@-	-1000; 252	PABPC1	2; 0	2; 0
chr3:129035116@-	-1000; 186	H1FX	0; 2	0; 2
chr19:49122547@+	-1000; 126	SPHK2	0; 2	0; 2
chr13:41635409@+	-1000; 200	WBP4	0; 2	0; 2
chrX:151999510@+	-1000; 75	NSDHL	0; 1	0; 1
chr9:95640303@-	-1000; 66	ZNF484	0; 1	0; 1
chr9:140100118@+	-1000; 55	NDOR1	0; 1	0; 1

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr6:166401114@+	-1000; 249	AL132661.1	0; 4	0; 4
chr17:7387865@+	-741; 109	POLR2A	3; 0	3; 0
chr12:54673914@-	-1000; 62	CBX5	0; 3	0; 3
chr8:101734314@-	-1000; 252	PABPC1	2; 0	2; 0
chr4:83295655@-	-1000; 103	HNRNPD	0; 1	0; 2
chr3:129035116@-	-1000; 186	H1FX	0; 2	0; 2
chr19:49122547@+	-1000; 126	SPHK2	0; 2	0; 2
chr13:41635409@+	-1000; 200	WBP4	0; 2	0; 2
chr12:21654698@+	-1000; 79	GOLT1B	1; 0	2; 0
chrX:151999510@+	-1000; 75	NSDHL	0; 1	0; 1

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 3UTR-inter

junction is at position zero.
upstream is regions of type: 3UTR
downstream is regions of type: inter, telo

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	890	5.13%	15.65%	87.43%	611	1.28242
anti	128	0.74%	2.25%	12.57%	88	0.184438
both	1018	5.87%	17.90%	100.00%	694	1.46686
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	941	5.11%	15.62%	87.70%	611	1.35591
anti	132	0.72%	2.19%	12.30%	88	0.190202
both	1073	5.83%	17.81%	100.00%	694	1.54611

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr16:18802989@-	-300; 667	ARL6IP1	12; 0	12; 0
chr17:4848945@-	-123; 1000	PFN1	11; 0	17; 0
chr21:44834393@-	-300; 1000	SIK1	8; 0	9; 0
chr1:100548933@+	-300; 1000	HIAT1	3; 5	3; 5
chr17:79845715@-	-144; 1000	THOC4	7; 0	8; 0
chr17:55757299@+	-195; 1000	MSI2	7; 0	7; 0
chr14:62214976@+	-300; 1000	HIF1A	7; 0	9; 0
chr9:124095121@+	-120; 1000	GSN	6; 0	7; 0
chr8:42978323@+	-152; 1000	AC113191.2	6; 0	7; 0
chr18:8639380@+	-300; 1000	RAB12	6; 0	6; 0

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr17:4848945@-	-123; 1000	PFN1	11; 0	17; 0
chr16:18802989@-	-300; 667	ARL6IP1	12; 0	12; 0
chr21:44834393@-	-300; 1000	SIK1	8; 0	9; 0
chr14:62214976@+	-300; 1000	HIF1A	7; 0	9; 0
chr17:79845715@-	-144; 1000	THOC4	7; 0	8; 0
chr1:100548933@+	-300; 1000	HIAT1	3; 5	3; 5
chr9:124095121@+	-120; 1000	GSN	6; 0	7; 0
chr8:42978323@+	-152; 1000	AC113191.2	6; 0	7; 0
chr17:79476997@-	-300; 1000	ACTG1	6; 0	7; 0
chr17:55757299@+	-195; 1000	MSI2	7; 0	7; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap inter-5

junction is at position zero.
upstream is regions of type: inter, telo
downstream is regions of type: ORF, intron, 3UTR, 5UTR, ncRNA

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	95	0.55%	1.67%	32.20%	69	0.446009
anti	200	1.15%	3.52%	67.80%	145	0.938967
both	295	1.70%	5.19%	100.00%	213	1.38498
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	100	0.54%	1.66%	32.47%	69	0.469484
anti	208	1.13%	3.45%	67.53%	145	0.976526
both	308	1.67%	5.11%	100.00%	213	1.44601

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 13	0; 15
chrUn_gl000220:109077@+	-758; 300	18S	9; 0	9; 0
chr8:128231332@-	-1000; 139	AC020688.1	7; 0	7; 0
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 6	0; 6
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	6; 0	9; 0
chr7:4811073@-	-1000; 300	AC092610.1	0; 4	0; 5
chr6:166401114@+	-1000; 249	AL132661.1	0; 4	0; 4
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 4	0; 4
chr3:49571651@-	-1000; 300	AC104452.1	0; 4	0; 4
chr13:30083551@+	-1000; 300	AL596114.1	0; 4	0; 4

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 13	0; 15
chrUn_gl000220:109077@+	-758; 300	18S	9; 0	9; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	6; 0	9; 0
chr8:128231332@-	-1000; 139	AC020688.1	7; 0	7; 0
chr2:20648680@-	-1000; 300	AC023137.2-ENSG00000247111	0; 6	0; 6
chr7:4811073@-	-1000; 300	AC092610.1	0; 4	0; 5
chr6:166401114@+	-1000; 249	AL132661.1	0; 4	0; 4
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 4	0; 4
chr3:49571651@-	-1000; 300	AC104452.1	0; 4	0; 4
chr13:30083551@+	-1000; 300	AL596114.1	0; 4	0; 4

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap 3-inter

junction is at position zero.
upstream is regions of type: ORF, intron, 3UTR, 5UTR, ncRNA
downstream is regions of type: inter, telo

[eps]

x-links and junctions distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [junctions] in map	[x-link sites] per unique [junction]
same	1225	7.06%	21.54%	82.99%	761	1.34615
anti	251	1.45%	4.41%	17.01%	155	0.275824
both	1476	8.50%	25.95%	100.00%	910	1.62198
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [junctions] in map	[single hits (=G+T), cDNA counts] per unique [junction]
same	1343	7.30%	22.29%	83.36%	761	1.47582
anti	268	1.46%	4.45%	16.64%	155	0.294505
both	1611	8.75%	26.74%	100.00%	910	1.77033

Top 10 junctions with largest x-link sites sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	97; 0	126; 0
chr7:5566780@-	-300; 1000	ACTB	21; 0	45; 0
chr1:169101767@-	-127; 1000	NME7	0; 20	0; 22
chr16:18802989@-	-300; 667	ARL6IP1	12; 0	12; 0
chr17:4848945@-	-123; 1000	PFN1	11; 0	17; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 9	0; 12
chrUn_gl000220:118417@+	-300; 1000	28S	8; 0	10; 0
chr21:44834393@-	-300; 1000	SIK1	8; 0	9; 0
chr1:100548933@+	-300; 1000	HIAT1	3; 5	3; 5
chr6:44221831@-	-300; 1000	SLC35B2	0; 7	0; 13

Top 10 junctions with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [junction]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr11:65271080@+	-300; 1000	MALAT1	97; 0	126; 0
chr7:5566780@-	-300; 1000	ACTB	21; 0	45; 0
chr1:169101767@-	-127; 1000	NME7	0; 20	0; 22
chr17:4848945@-	-123; 1000	PFN1	11; 0	17; 0
chr6:44221831@-	-300; 1000	SLC35B2	0; 7	0; 13
chr16:18802989@-	-300; 667	ARL6IP1	12; 0	12; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 9	0; 12
chrUn_gl000220:118417@+	-300; 1000	28S	8; 0	10; 0
chr21:44834393@-	-300; 1000	SIK1	8; 0	9; 0
chr14:62214976@+	-300; 1000	HIF1A	7; 0	9; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.

RNAmap "BP best in intron"

BP is at position zero.
upstream is usptream of branch point
downstream is downstream of branch point

[eps]

x-links and BPs distributions

strand	[x-link sites] used in map	[x-link sites] % of total	[x-link sites] % of used in any map	[x-link sites] % of used in map	unique [BPs] in map	[x-link sites] per unique [BP]
same	558	3.21%	9.81%	93.47%	522	0.996429
anti	39	0.22%	0.69%	6.53%	38	0.0696429
both	597	3.44%	10.50%	100.00%	560	1.06607
strand	[single hits (=G+T), cDNA counts] used in map	[single hits (=G+T), cDNA counts] % of total	[single hits (=G+T), cDNA counts] % of used in any map	[single hits (=G+T), cDNA counts] % of used in map	unique [BPs] in map	[single hits (=G+T), cDNA counts] per unique [BP]
same	567	3.08%	9.41%	93.10%	522	1.0125
anti	42	0.23%	0.70%	6.90%	38	0.075
both	609	3.31%	10.11%	100.00%	560	1.0875

Top 10 BPs with largest x-link sites sum (both strands)

position of [BP]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr5:43543440@-	-300; 100	PAIP1	5; 0	5; 0
chr2:191537788@+	-300; 36	NAB1	4; 0	4; 0
chr5:65318955@+	-300; 100	ERBB2IP	3; 0	3; 0
chr11:71710833@+	-300; 100	IL18BP	3; 0	3; 0
chr1:70697488@+	-300; 100	SFRS11	3; 0	3; 0
chrX:2864196@-	-300; 22	ARSE	2; 0	2; 0
chr6:136499677@+	-300; 100	PDE7B	2; 0	2; 0
chr6:76357382@+	-300; 62	SENP6	2; 0	2; 0
chr5:179041984@-	-268; 25	HNRNPH1	2; 0	2; 0
chr5:106723912@-	-300; 100	EFNA5	2; 0	2; 0

Top 10 BPs with largest [single hits (=G+T), cDNA counts] sum (both strands)

position of [BP]	span (upstream; downstream)	associated gene	[x-link sites] (same; anti)	[single hits (=G+T), cDNA counts] (same; anti)
chr5:43543440@-	-300; 100	PAIP1	5; 0	5; 0
chr2:191537788@+	-300; 36	NAB1	4; 0	4; 0
chr12:133213075@-	-300; 100	POLE	0; 2	0; 4
chr5:65318955@+	-300; 100	ERBB2IP	3; 0	3; 0
chr11:71710833@+	-300; 100	IL18BP	3; 0	3; 0
chr1:70697488@+	-300; 100	SFRS11	3; 0	3; 0
chrX:2864196@-	-300; 22	ARSE	2; 0	2; 0
chr7:55459161@+	-300; 100	LANCL2	1; 0	2; 0
chr7:30670981@+	-300; 80	GARS	1; 0	2; 0
chr6:136499677@+	-300; 100	PDE7B	2; 0	2; 0

Download full junction summary list in tab-delimited format.
Download full list of x-links used for RNAmap in tab-delimited format.