Parameters
input_file: 20090724_LUd3_2_hg19_ensembl59_S_iCLIP_TIA1_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: 32155
[x-link sites] used in any map: 10336 (32.14%)
[single hits (=G+T), cDNA counts] total: 32155
[single hits (=G+T), cDNA counts] used in any map: 10822 (32.11%)

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	2824	8.78%	27.32%	2896	8.59%	26.76%
intron-exon	-300; 300	2295	7.14%	22.20%	2357	6.99%	21.78%
5-ncRNA	-1000; 300	566	1.76%	5.48%	614	1.82%	5.67%
ncRNA-3	-300; 1000	666	2.07%	6.44%	747	2.22%	6.90%
ORF-3UTR	-300; 300	1636	5.09%	15.83%	1728	5.13%	15.97%
5UTR-ORF	-300; 300	83	0.26%	0.80%	85	0.25%	0.79%
inter-5UTR	-1000; 300	140	0.44%	1.35%	142	0.42%	1.31%
3UTR-inter	-300; 1000	1741	5.41%	16.84%	1828	5.42%	16.89%
inter-5	-1000; 300	499	1.55%	4.83%	532	1.58%	4.92%
3-inter	-300; 1000	2375	7.39%	22.98%	2572	7.63%	23.77%
BP best in intron	-300; 100	1235	3.84%	11.95%	1283	3.81%	11.86%

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	2739	8.52%	26.50%	96.99%	2502	1.07076
anti	85	0.26%	0.82%	3.01%	59	0.0332291
both	2824	8.78%	27.32%	100.00%	2558	1.10399
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	2798	8.30%	25.85%	96.62%	2502	1.09382
anti	98	0.29%	0.91%	3.38%	59	0.0383112
both	2896	8.59%	26.76%	100.00%	2558	1.13213

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; 15	0; 26
chr7:128411528@+	-300; 107	CALU	10; 0	13; 0
chr3:41281934@+	-300; 300	CTNNB1	9; 0	9; 0
chr12:50158717@+	-300; 300	TMBIM6	9; 0	11; 0
chr6:18225699@-	-124; 192	DEK	7; 0	8; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 7	0; 7
chr5:10401598@+	-300; 185	MARCH6	7; 0	7; 0
chr7:90001542@+	-37; 300	GTPBP10	6; 0	6; 0
chr5:179048241@-	-78; 103	HNRNPH1	6; 0	7; 0
chr7:139025365@+	-85; 256	C7orf55	5; 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)
chr1:45976739@+	-281; 300	MMACHC	0; 15	0; 26
chr7:128411528@+	-300; 107	CALU	10; 0	13; 0
chr12:50158717@+	-300; 300	TMBIM6	9; 0	11; 0
chr3:41281934@+	-300; 300	CTNNB1	9; 0	9; 0
chr6:18225699@-	-124; 192	DEK	7; 0	8; 0
chr5:179048241@-	-78; 103	HNRNPH1	6; 0	7; 0
chr5:177637967@-	-300; 300	AGXT2L2	0; 7	0; 7
chr5:10401598@+	-300; 185	MARCH6	7; 0	7; 0
chr7:139025365@+	-85; 256	C7orf55	5; 0	6; 0
chr7:90001542@+	-37; 300	GTPBP10	6; 0	6; 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	2225	6.92%	21.53%	96.95%	1997	1.08273
anti	70	0.22%	0.68%	3.05%	59	0.0340633
both	2295	7.14%	22.20%	100.00%	2055	1.11679
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	2287	6.79%	21.13%	97.03%	1997	1.1129
anti	70	0.21%	0.65%	2.97%	59	0.0340633
both	2357	6.99%	21.78%	100.00%	2055	1.14696

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)
chr15:45009804@+	-300; 277	B2M	18; 0	19; 0
chr9:131456919@+	-292; 300	SET	17; 0	22; 0
chr17:1248792@-	-300; 300	YWHAE	6; 0	7; 0
chr16:29821927@-	-300; 92	AC009133.4	0; 6	0; 6
chr15:69072480@-	-134; 300	ANP32A	6; 0	6; 0
chr10:112657785@+	-300; 300	PDCD4	6; 0	11; 0
chr1:26227577@-	-160; 260	STMN1	6; 0	6; 0
chr5:179041959@-	-293; 300	HNRNPH1	5; 0	6; 0
chr2:47387942@-	-300; 300	CALM2	5; 0	5; 0
chr11:2966875@-	-300; 300	NAP1L4	5; 0	5; 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	17; 0	22; 0
chr15:45009804@+	-300; 277	B2M	18; 0	19; 0
chr10:112657785@+	-300; 300	PDCD4	6; 0	11; 0
chr17:1248792@-	-300; 300	YWHAE	6; 0	7; 0
chr5:180665662@-	-187; 212	GNB2L1	4; 0	6; 0
chr5:179041959@-	-293; 300	HNRNPH1	5; 0	6; 0
chr16:29821927@-	-300; 92	AC009133.4	0; 6	0; 6
chr15:69072480@-	-134; 300	ANP32A	6; 0	6; 0
chr11:4139549@+	-300; 71	RRM1	5; 0	6; 0
chr1:26227577@-	-160; 260	STMN1	6; 0	6; 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	298	0.93%	2.88%	52.65%	166	0.823204
anti	268	0.83%	2.59%	47.35%	196	0.740331
both	566	1.76%	5.48%	100.00%	362	1.56354
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	337	1.00%	3.11%	54.89%	166	0.930939
anti	277	0.82%	2.56%	45.11%	196	0.765193
both	614	1.82%	5.67%	100.00%	362	1.69613

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	69; 0	84; 0
chr17:57918626@+	-338; 36	hsa-mir-21	13; 0	15; 0
chrUn_gl000220:109077@+	-758; 300	18S	12; 0	13; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 12	0; 12
chr13:30083551@+	-1000; 300	AL596114.1	0; 10	0; 11
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	8; 0	13; 0
chrUn_gl000220:113347@+	-585; 300	28S	7; 0	7; 0
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 7	0; 7
chr8:128231332@-	-1000; 139	AC020688.1	6; 0	6; 0
chr3:129034234@+	-1000; 123	RP13-685P2.5	0; 6	0; 7

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	69; 0	84; 0
chr17:57918626@+	-338; 36	hsa-mir-21	13; 0	15; 0
chrUn_gl000220:109077@+	-758; 300	18S	12; 0	13; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	8; 0	13; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 12	0; 12
chr13:30083551@+	-1000; 300	AL596114.1	0; 10	0; 11
chrUn_gl000220:113347@+	-585; 300	28S	7; 0	7; 0
chr3:129034234@+	-1000; 123	RP13-685P2.5	0; 6	0; 7
chr17:74730198@+	-119; 300	AC005837.2	0; 6	0; 7
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 7	0; 7

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	438	1.36%	4.24%	65.77%	237	1.08685
anti	228	0.71%	2.21%	34.23%	168	0.565757
both	666	2.07%	6.44%	100.00%	403	1.65261
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	509	1.51%	4.70%	68.14%	237	1.26303
anti	238	0.71%	2.20%	31.86%	168	0.590571
both	747	2.22%	6.90%	100.00%	403	1.8536

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	99; 0	136; 0
chrUn_gl000220:110946@+	-300; 539	18S	29; 0	38; 0
chrUn_gl000220:118417@+	-300; 1000	28S	13; 0	19; 0
chr3:14530617@-	-300; 1000	GRIP2	0; 9	0; 9
chr8:144939422@+	-300; 1000	AC105049.1	0; 6	0; 6
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	6; 0	8; 0
chr3:47705424@+	-155; 1000	RP11-395P16.1	0; 6	0; 6
chr10:112658486@-	-300; 1000	NCRNA00081	0; 6	0; 11
chr1:17733878@+	-33; 1000	RP1-20B21.4	0; 6	0; 6
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	5; 0	7; 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)
chr11:65271080@+	-300; 1000	MALAT1	99; 0	136; 0
chrUn_gl000220:110946@+	-300; 539	18S	29; 0	38; 0
chrUn_gl000220:118417@+	-300; 1000	28S	13; 0	19; 0
chr10:112658486@-	-300; 1000	NCRNA00081	0; 6	0; 11
chr3:14530617@-	-300; 1000	GRIP2	0; 9	0; 9
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	6; 0	8; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	5; 0	7; 0
chr8:144939422@+	-300; 1000	AC105049.1	0; 6	0; 6
chr3:47705424@+	-155; 1000	RP11-395P16.1	0; 6	0; 6
chr1:148604906@-	-83; 1000	U1-ENSG00000207205	5; 0	6; 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	1613	5.02%	15.61%	98.59%	898	1.76092
anti	23	0.07%	0.22%	1.41%	20	0.0251092
both	1636	5.09%	15.83%	100.00%	916	1.78603
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	1704	5.06%	15.75%	98.61%	898	1.86026
anti	24	0.07%	0.22%	1.39%	20	0.0262009
both	1728	5.13%	15.97%	100.00%	916	1.88646

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	25; 0	40; 0
chr3:149087560@-	-53; 300	TM4SF1	20; 0	24; 0
chr1:54497690@-	-144; 172	TMEM59	17; 0	20; 0
chr1:35650053@-	-70; 300	SFPQ	15; 0	16; 0
chr6:30692174@+	-300; 300	TUBB	12; 0	13; 0
chr21:27253823@-	-129; 300	APP	12; 0	13; 0
chr7:148700882@-	-209; 300	PDIA4	11; 0	12; 0
chr5:179156650@+	-145; 300	CANX	11; 0	11; 0
chr22:38881684@-	-300; 300	DDX17	11; 0	13; 0
chr14:62213803@+	-76; 300	HIF1A	11; 0	11; 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	25; 0	40; 0
chr3:149087560@-	-53; 300	TM4SF1	20; 0	24; 0
chr1:54497690@-	-144; 172	TMEM59	17; 0	20; 0
chr1:35650053@-	-70; 300	SFPQ	15; 0	16; 0
chr6:30692174@+	-300; 300	TUBB	12; 0	13; 0
chr22:38881684@-	-300; 300	DDX17	11; 0	13; 0
chr21:27253823@-	-129; 300	APP	12; 0	13; 0
chr7:148700882@-	-209; 300	PDIA4	11; 0	12; 0
chr5:32601448@+	-169; 300	SUB1	10; 0	12; 0
chrX:102931085@-	-300; 300	MORF4L2	10; 0	11; 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	72	0.22%	0.70%	86.75%	69	0.935065
anti	11	0.03%	0.11%	13.25%	8	0.142857
both	83	0.26%	0.80%	100.00%	77	1.07792
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	74	0.22%	0.68%	87.06%	69	0.961039
anti	11	0.03%	0.10%	12.94%	8	0.142857
both	85	0.25%	0.79%	100.00%	77	1.1039

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)
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 3	0; 3
chr7:135612307@+	-300; 127	AC015987.2	0; 2	0; 2
chr2:136873508@-	-152; 300	CXCR4	2; 0	2; 0
chr2:20251280@-	-254; 55	LAPTM4A	2; 0	2; 0
chr17:4851688@-	-300; 66	PFN1	2; 0	2; 0
chrX:106960040@-	-162; 61	TSC22D3	1; 0	1; 0
chrX:48434573@+	-51; 117	RBM3	1; 0	1; 0
chr9:117267080@-	-300; 300	DFNB31	1; 0	1; 0
chr9:89561693@-	-205; 300	GAS1	1; 0	1; 0
chr8:119123284@-	-300; 300	EXT1	1; 0	2; 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)
chr1:168216282@-	-149; 181	ANKRD36BL1	0; 3	0; 3
chr8:119123284@-	-300; 300	EXT1	1; 0	2; 0
chr7:135612307@+	-300; 127	AC015987.2	0; 2	0; 2
chr3:33155569@+	-50; 235	CRTAP	1; 0	2; 0
chr2:136873508@-	-152; 300	CXCR4	2; 0	2; 0
chr2:20251280@-	-254; 55	LAPTM4A	2; 0	2; 0
chr17:4851688@-	-300; 66	PFN1	2; 0	2; 0
chrX:106960040@-	-162; 61	TSC22D3	1; 0	1; 0
chrX:48434573@+	-51; 117	RBM3	1; 0	1; 0
chr9:117267080@-	-300; 300	DFNB31	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	48	0.15%	0.46%	34.29%	39	0.428571
anti	92	0.29%	0.89%	65.71%	73	0.821429
both	140	0.44%	1.35%	100.00%	112	1.25
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	49	0.15%	0.45%	34.51%	39	0.4375
anti	93	0.28%	0.86%	65.49%	73	0.830357
both	142	0.42%	1.31%	100.00%	112	1.26786

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)
chr8:101734314@-	-1000; 252	PABPC1	10; 0	11; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 10	0; 10
chr15:89878025@-	-1000; 61	POLG	0; 3	0; 3
chr8:33370702@-	-1000; 286	C8orf41	0; 2	0; 2
chr8:71485680@+	-1000; 300	AC120194.1	0; 2	0; 2
chr5:34919093@-	-1000; 234	RAD1	0; 2	0; 2
chr20:47894962@-	-1000; 248	ZNFX1	0; 2	0; 2
chr13:41635409@+	-1000; 200	WBP4	0; 2	0; 2
chr11:62623517@+	-1000; 112	SLC3A2	0; 2	0; 2
chr1:168216580@-	-1000; 149	ANKRD36BL1	0; 2	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)
chr8:101734314@-	-1000; 252	PABPC1	10; 0	11; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 10	0; 10
chr15:89878025@-	-1000; 61	POLG	0; 3	0; 3
chr8:33370702@-	-1000; 286	C8orf41	0; 2	0; 2
chr8:71485680@+	-1000; 300	AC120194.1	0; 2	0; 2
chr6:30294255@+	-1000; 258	TRIM39	0; 1	0; 2
chr5:34919093@-	-1000; 234	RAD1	0; 2	0; 2
chr20:47894962@-	-1000; 248	ZNFX1	0; 2	0; 2
chr13:41635409@+	-1000; 200	WBP4	0; 2	0; 2
chr11:62623517@+	-1000; 112	SLC3A2	0; 2	0; 2

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	1502	4.67%	14.53%	86.27%	921	1.40901
anti	239	0.74%	2.31%	13.73%	151	0.224203
both	1741	5.41%	16.84%	100.00%	1066	1.63321
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	1575	4.67%	14.55%	86.16%	921	1.47749
anti	253	0.75%	2.34%	13.84%	151	0.237336
both	1828	5.42%	16.89%	100.00%	1066	1.71482

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)
chr13:113978542@-	-129; 1000	GRTP1	0; 18	0; 19
chr19:39220830@-	-300; 1000	CAPN12	0; 16	0; 16
chr16:18802989@-	-300; 667	ARL6IP1	13; 0	14; 0
chr9:124095121@+	-120; 1000	GSN	11; 0	12; 0
chr17:79476997@-	-300; 1000	ACTG1	11; 0	12; 0
chr8:128753674@+	-235; 1000	MYC	10; 0	11; 0
chr11:65622306@-	-249; 1000	CFL1	10; 0	13; 0
chr19:13055304@+	-289; 674	CALR	9; 0	10; 0
chr17:79845715@-	-144; 1000	THOC4	9; 0	13; 0
chr13:30083545@-	-300; 1000	SLC7A1	9; 0	10; 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)
chr13:113978542@-	-129; 1000	GRTP1	0; 18	0; 19
chr19:39220830@-	-300; 1000	CAPN12	0; 16	0; 16
chr16:18802989@-	-300; 667	ARL6IP1	13; 0	14; 0
chr17:79845715@-	-144; 1000	THOC4	9; 0	13; 0
chr11:65622306@-	-249; 1000	CFL1	10; 0	13; 0
chr9:124095121@+	-120; 1000	GSN	11; 0	12; 0
chr17:79476997@-	-300; 1000	ACTG1	11; 0	12; 0
chr8:128753674@+	-235; 1000	MYC	10; 0	11; 0
chr3:145787225@-	-300; 127	PLOD2	8; 0	10; 0
chr19:13055304@+	-289; 674	CALR	9; 0	10; 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	147	0.46%	1.42%	29.46%	108	0.415254
anti	352	1.09%	3.41%	70.54%	247	0.99435
both	499	1.55%	4.83%	100.00%	354	1.4096
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	165	0.49%	1.52%	31.02%	108	0.466102
anti	367	1.09%	3.39%	68.98%	247	1.03672
both	532	1.58%	4.92%	100.00%	354	1.50282

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; 21	0; 27
chrUn_gl000220:109077@+	-758; 300	18S	12; 0	13; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 12	0; 12
chr8:101734314@-	-1000; 252	PABPC1	10; 0	11; 0
chr6:166401114@+	-1000; 249	AL132661.1	0; 10	0; 10
chr13:30083551@+	-1000; 300	AL596114.1	0; 10	0; 11
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	8; 0	13; 0
chrUn_gl000220:113347@+	-585; 300	28S	7; 0	7; 0
chr1:234742753@+	-1000; 300	RP4-781K5.2	0; 7	0; 7
chr8:128231332@-	-1000; 139	AC020688.1	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)
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 21	0; 27
chrUn_gl000220:109077@+	-758; 300	18S	12; 0	13; 0
chr11:62609280@-	-1000; 95	U2-ENSG00000222328	8; 0	13; 0
chr5:137088165@+	-1000; 289	RP11-381K20.4	0; 12	0; 12
chr8:101734314@-	-1000; 252	PABPC1	10; 0	11; 0
chr13:30083551@+	-1000; 300	AL596114.1	0; 10	0; 11
chr6:166401114@+	-1000; 249	AL132661.1	0; 10	0; 10
chrUn_gl000220:113347@+	-585; 300	28S	7; 0	7; 0
chr3:129034234@+	-1000; 123	RP13-685P2.5	0; 6	0; 7
chr17:74730198@+	-119; 300	AC005837.2	0; 6	0; 7

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	1924	5.98%	18.61%	81.01%	1122	1.37429
anti	451	1.40%	4.36%	18.99%	289	0.322143
both	2375	7.39%	22.98%	100.00%	1400	1.69643
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	2100	6.23%	19.40%	81.65%	1122	1.5
anti	472	1.40%	4.36%	18.35%	289	0.337143
both	2572	7.63%	23.77%	100.00%	1400	1.83714

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	99; 0	136; 0
chrUn_gl000220:110946@+	-300; 539	18S	29; 0	38; 0
chr7:5566780@-	-300; 1000	ACTB	26; 0	57; 0
chr1:169101767@-	-127; 1000	NME7	0; 20	0; 20
chr13:113978542@-	-129; 1000	GRTP1	0; 18	0; 19
chr19:39220830@-	-300; 1000	CAPN12	0; 16	0; 16
chr1:153516087@-	-156; 923	S100A4	14; 0	19; 0
chrUn_gl000220:118417@+	-300; 1000	28S	13; 0	19; 0
chr16:18802989@-	-300; 667	ARL6IP1	13; 0	14; 0
chr9:124095121@+	-120; 1000	GSN	11; 0	12; 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)
chr11:65271080@+	-300; 1000	MALAT1	99; 0	136; 0
chr7:5566780@-	-300; 1000	ACTB	26; 0	57; 0
chrUn_gl000220:110946@+	-300; 539	18S	29; 0	38; 0
chr1:169101767@-	-127; 1000	NME7	0; 20	0; 20
chrUn_gl000220:118417@+	-300; 1000	28S	13; 0	19; 0
chr13:113978542@-	-129; 1000	GRTP1	0; 18	0; 19
chr1:153516087@-	-156; 923	S100A4	14; 0	19; 0
chr19:39220830@-	-300; 1000	CAPN12	0; 16	0; 16
chr16:18802989@-	-300; 667	ARL6IP1	13; 0	14; 0
chr17:79845715@-	-144; 1000	THOC4	9; 0	13; 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	1202	3.74%	11.63%	97.33%	1131	1.03621
anti	33	0.10%	0.32%	2.67%	29	0.0284483
both	1235	3.84%	11.95%	100.00%	1160	1.06466
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	1250	3.71%	11.55%	97.43%	1131	1.07759
anti	33	0.10%	0.30%	2.57%	29	0.0284483
both	1283	3.81%	11.86%	100.00%	1160	1.10603

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)
chr5:10401919@+	-300; 100	MARCH6	8; 0	8; 0
chr9:86584384@-	-300; 90	HNRNPK	5; 0	7; 0
chr11:4139437@+	-300; 100	RRM1	5; 0	6; 0
chr5:111067169@-	-300; 100	C5orf13	4; 0	4; 0
chr12:32861040@+	-300; 44	DNM1L	0; 4	0; 4
chr5:179048854@-	-300; 100	HNRNPH1	3; 0	4; 0
chr17:38288172@+	-113; 100	MSL1	3; 0	3; 0
chr14:70237083@+	-300; 98	SFRS5	3; 0	3; 0
chr13:111303470@-	-300; 24	CARS2	3; 0	3; 0
chr1:1326494@-	-300; 100	CCNL2	3; 0	3; 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)
chr5:10401919@+	-300; 100	MARCH6	8; 0	8; 0
chr9:86584384@-	-300; 90	HNRNPK	5; 0	7; 0
chr11:4139437@+	-300; 100	RRM1	5; 0	6; 0
chr5:179048854@-	-300; 100	HNRNPH1	3; 0	4; 0
chr5:111067169@-	-300; 100	C5orf13	4; 0	4; 0
chr12:32861040@+	-300; 44	DNM1L	0; 4	0; 4
chrX:153225889@-	-300; 25	HCFC1	1; 0	3; 0
chr5:179045370@-	-300; 47	HNRNPH1	2; 0	3; 0
chr3:180326196@+	-178; 100	TTC14	2; 0	3; 0
chr2:61413393@+	-229; 100	AHSA2	2; 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.