Parameters
input_file: 20090724_LUe5_1_hg19_ensembl59_S_iCLIP_TDP-43_Brain-C25_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: 19023
[x-link sites] used in any map: 4708 (24.75%)
[single hits (=G+T), cDNA counts] total: 19023
[single hits (=G+T), cDNA counts] used in any map: 5538 (26.64%)

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	923	4.85%	19.60%	962	4.63%	17.37%
intron-exon	-300; 300	1266	6.66%	26.89%	1328	6.39%	23.98%
5-ncRNA	-1000; 300	935	4.92%	19.86%	1478	7.11%	26.69%
ncRNA-3	-300; 1000	661	3.47%	14.04%	816	3.93%	14.73%
ORF-3UTR	-300; 300	277	1.46%	5.88%	291	1.40%	5.25%
5UTR-ORF	-300; 300	65	0.34%	1.38%	73	0.35%	1.32%
inter-5UTR	-1000; 300	91	0.48%	1.93%	97	0.47%	1.75%
3UTR-inter	-300; 1000	329	1.73%	6.99%	337	1.62%	6.09%
inter-5	-1000; 300	694	3.65%	14.74%	1130	5.44%	20.40%
3-inter	-300; 1000	670	3.52%	14.23%	758	3.65%	13.69%
BP best in intron	-300; 100	515	2.71%	10.94%	546	2.63%	9.86%

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	889	4.67%	18.88%	96.32%	762	1.11824
anti	34	0.18%	0.72%	3.68%	33	0.0427673
both	923	4.85%	19.60%	100.00%	795	1.16101
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	927	4.46%	16.74%	96.36%	762	1.16604
anti	35	0.17%	0.63%	3.64%	33	0.0440252
both	962	4.63%	17.37%	100.00%	795	1.21006

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)
chr17:72951885@-	-83; 300	C17orf28	7; 0	7; 0
chr3:116163722@-	-78; 300	LSAMP	6; 0	7; 0
chr22:38687371@-	-285; 177	CSNK1E	5; 0	5; 0
chr7:99951635@+	-160; 300	PILRB	4; 0	5; 0
chr6:17285396@+	-57; 300	RBM24	4; 0	4; 0
chr5:179048842@-	-53; 222	HNRNPH1	4; 0	4; 0
chr20:33969719@-	-54; 300	UQCC	4; 0	8; 0
chr1:9804451@-	-125; 194	CLSTN1	4; 0	4; 0
chr1:9795941@-	-79; 134	CLSTN1	4; 0	6; 0
chrX:28606164@+	-300; 300	IL1RAPL1	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)
chr20:33969719@-	-54; 300	UQCC	4; 0	8; 0
chr3:116163722@-	-78; 300	LSAMP	6; 0	7; 0
chr17:72951885@-	-83; 300	C17orf28	7; 0	7; 0
chr1:9795941@-	-79; 134	CLSTN1	4; 0	6; 0
chr7:99951635@+	-160; 300	PILRB	4; 0	5; 0
chr22:38687371@-	-285; 177	CSNK1E	5; 0	5; 0
chr7:139025365@+	-85; 256	C7orf55	3; 0	4; 0
chr6:17285396@+	-57; 300	RBM24	4; 0	4; 0
chr5:179048842@-	-53; 222	HNRNPH1	4; 0	4; 0
chr1:9804451@-	-125; 194	CLSTN1	4; 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 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	1212	6.37%	25.74%	95.73%	1017	1.1359
anti	54	0.28%	1.15%	4.27%	50	0.0506092
both	1266	6.66%	26.89%	100.00%	1067	1.1865
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	1274	6.13%	23.00%	95.93%	1017	1.194
anti	54	0.26%	0.98%	4.07%	50	0.0506092
both	1328	6.39%	23.98%	100.00%	1067	1.24461

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)
chr9:97055255@+	-175; 300	ZNF169	7; 0	7; 0
chr5:94026899@+	-300; 231	ANKRD32	6; 0	6; 0
chr22:39715115@-	-130; 42	RPL3	6; 0	12; 0
chr1:84413308@-	-300; 251	TTLL7	5; 0	6; 0
chrX:47067960@+	-300; 300	UBA1	4; 0	4; 0
chr2:32822817@+	-300; 109	BIRC6	4; 0	4; 0
chr11:103104762@+	-300; 63	DYNC2H1	4; 0	4; 0
chr1:182353857@-	-300; 300	GLUL	4; 0	4; 0
chr9:80942966@+	-300; 69	PSAT1	3; 0	3; 0
chr8:27462851@-	-300; 206	CLU	3; 0	4; 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)
chr22:39715115@-	-130; 42	RPL3	6; 0	12; 0
chr9:97055255@+	-175; 300	ZNF169	7; 0	7; 0
chr5:94026899@+	-300; 231	ANKRD32	6; 0	6; 0
chr1:84413308@-	-300; 251	TTLL7	5; 0	6; 0
chr11:18425240@+	-300; 59	LDHA	3; 0	5; 0
chrX:47067960@+	-300; 300	UBA1	4; 0	4; 0
chr8:27462851@-	-300; 206	CLU	3; 0	4; 0
chr5:136957814@-	-300; 300	KLHL3	3; 0	4; 0
chr3:110793741@+	-300; 174	PVRL3	3; 0	4; 0
chr2:32822817@+	-300; 109	BIRC6	4; 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 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	822	4.32%	17.46%	87.91%	353	1.83893
anti	113	0.59%	2.40%	12.09%	94	0.252796
both	935	4.92%	19.86%	100.00%	447	2.09172
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	1359	6.54%	24.54%	91.95%	353	3.04027
anti	119	0.57%	2.15%	8.05%	94	0.266219
both	1478	7.11%	26.69%	100.00%	447	3.30649

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_gl000220:109077@+	-758; 300	18S	103; 0	301; 0
chr1:109642814@+	-1000; 210	snoU2-25	58; 0	146; 0
chrUn_gl000220:113347@+	-585; 300	28S	54; 0	81; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	13; 0	26; 0
chr15:25230246@+	-1000; 33	SNORD64-ENSG00000209418	12; 0	42; 0
chr11:65269806@+	-1000; 29	MALAT1	11; 0	11; 0
chr7:80962916@+	-1000; 115	AC004866.1-ENSG00000239843	8; 0	11; 0
chr15:25346721@+	-990; 46	SNORD116-ENSG00000251896	8; 0	10; 0
chr15:25344645@+	-872; 48	SNORD116-ENSG00000251815	8; 0	9; 0
chr15:25342809@+	-1000; 46	SNORD116-ENSG00000252326	8; 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)
chrUn_gl000220:109077@+	-758; 300	18S	103; 0	301; 0
chr1:109642814@+	-1000; 210	snoU2-25	58; 0	146; 0
chrUn_gl000220:113347@+	-585; 300	28S	54; 0	81; 0
chr15:25230246@+	-1000; 33	SNORD64-ENSG00000209418	12; 0	42; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	13; 0	26; 0
chr15:25336932@+	-886; 46	SNORD116-ENSG00000207375	5; 0	19; 0
chr1:8266656@-	-1000; 82	U1-ENSG00000200975	2; 0	16; 0
chr22:29729246@-	-503; 48	AP1B1, SNORD125	7; 0	15; 0
chr15:25332808@+	-522; 46	SNORD116-ENSG00000207259	5; 0	12; 0
chr7:80962916@+	-1000; 115	AC004866.1-ENSG00000239843	8; 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 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	506	2.66%	10.75%	76.55%	258	1.42938
anti	155	0.81%	3.29%	23.45%	99	0.437853
both	661	3.47%	14.04%	100.00%	354	1.86723
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	636	3.06%	11.48%	77.94%	258	1.79661
anti	180	0.87%	3.25%	22.06%	99	0.508475
both	816	3.93%	14.73%	100.00%	354	2.30508

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_gl000220:110946@+	-300; 539	18S	38; 0	46; 0
chrUn_gl000220:118417@+	-300; 1000	28S	25; 0	54; 0
chr11:65271080@+	-300; 1000	MALAT1	21; 0	22; 0
chr1:109643234@+	-210; 1000	snoU2-25	15; 0	22; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	13; 0	17; 0
chrY:10036111@-	-300; 1000	RN18S1	0; 12	0; 16
chr18:77773065@+	-110; 1000	AC090360.1	11; 0	17; 0
chr3:160232693@-	-165; 362	KPNA4, snoU90	9; 0	12; 0
chr2:133014537@-	-58; 1000	NCRNA00164, hsa-mir-663b	8; 0	10; 0
chr4:144257786@-	-255; 1000	AC097658.1	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)
chrUn_gl000220:118417@+	-300; 1000	28S	25; 0	54; 0
chrUn_gl000220:110946@+	-300; 539	18S	38; 0	46; 0
chr11:65271080@+	-300; 1000	MALAT1	21; 0	22; 0
chr1:109643234@+	-210; 1000	snoU2-25	15; 0	22; 0
chr18:77773065@+	-110; 1000	AC090360.1	11; 0	17; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	13; 0	17; 0
chrY:10036111@-	-300; 1000	RN18S1	0; 12	0; 16
chr4:144257786@-	-255; 1000	AC097658.1	0; 7	0; 13
chr3:160232693@-	-165; 362	KPNA4, snoU90	9; 0	12; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	6; 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 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	264	1.39%	5.61%	95.31%	206	1.23944
anti	13	0.07%	0.28%	4.69%	7	0.0610329
both	277	1.46%	5.88%	100.00%	213	1.30047
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	277	1.33%	5.00%	95.19%	206	1.30047
anti	14	0.07%	0.25%	4.81%	7	0.0657277
both	291	1.40%	5.25%	100.00%	213	1.3662

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)
chr16:67472427@-	-82; 253	ATP6V0D1	13; 0	16; 0
chrX:139865739@-	-300; 158	CDR1	0; 7	0; 8
chr17:79477712@-	-73; 300	ACTG1	4; 0	4; 0
chr9:115232824@+	-57; 300	HSDL2	3; 0	3; 0
chr4:176554594@-	-300; 255	GPM6A	3; 0	3; 0
chr2:27599586@+	-57; 204	SNX17	3; 0	3; 0
chr18:9954208@+	-80; 300	VAPA	3; 0	3; 0
chr1:169100793@+	-132; 300	ATP1B1	3; 0	3; 0
chr1:78024416@+	-65; 300	AK5	3; 0	3; 0
chr8:143694438@-	-300; 297	ARC	2; 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)
chr16:67472427@-	-82; 253	ATP6V0D1	13; 0	16; 0
chrX:139865739@-	-300; 158	CDR1	0; 7	0; 8
chr17:79477712@-	-73; 300	ACTG1	4; 0	4; 0
chr9:115232824@+	-57; 300	HSDL2	3; 0	3; 0
chr4:176554594@-	-300; 255	GPM6A	3; 0	3; 0
chr2:27599586@+	-57; 204	SNX17	3; 0	3; 0
chr18:9954208@+	-80; 300	VAPA	3; 0	3; 0
chr1:182352027@-	-300; 300	GLUL	2; 0	3; 0
chr1:169100793@+	-132; 300	ATP1B1	3; 0	3; 0
chr1:78024416@+	-65; 300	AK5	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 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	60	0.32%	1.27%	92.31%	45	1.2766
anti	5	0.03%	0.11%	7.69%	2	0.106383
both	65	0.34%	1.38%	100.00%	47	1.38298
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	68	0.33%	1.23%	93.15%	45	1.44681
anti	5	0.02%	0.09%	6.85%	2	0.106383
both	73	0.35%	1.32%	100.00%	47	1.55319

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)
chr4:71588290@+	-290; 89	RUFY3	6; 0	7; 0
chrX:139866530@-	-96; 300	CDR1	0; 4	0; 4
chr6:31508971@-	-66; 265	BAT1	3; 0	6; 0
chr12:121093613@+	-256; 231	CABP1	3; 0	3; 0
chrX:51149868@+	-51; 300	CXorf67	2; 0	3; 0
chr4:158141875@+	-70; 203	GRIA2	2; 0	2; 0
chr19:49926595@-	-51; 64	PTH2	2; 0	3; 0
chr17:47755471@-	-62; 89	SPOP	2; 0	2; 0
chr15:91769493@+	-196; 225	SV2B	2; 0	2; 0
chr12:30906696@-	-300; 210	CAPRIN2	2; 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)
chr4:71588290@+	-290; 89	RUFY3	6; 0	7; 0
chr6:31508971@-	-66; 265	BAT1	3; 0	6; 0
chrX:139866530@-	-96; 300	CDR1	0; 4	0; 4
chrX:51149868@+	-51; 300	CXorf67	2; 0	3; 0
chr19:49926595@-	-51; 64	PTH2	2; 0	3; 0
chr14:86087858@+	-188; 300	FLRT2	1; 0	3; 0
chr12:121093613@+	-256; 231	CABP1	3; 0	3; 0
chr4:158141875@+	-70; 203	GRIA2	2; 0	2; 0
chr17:47755471@-	-62; 89	SPOP	2; 0	2; 0
chr15:91769493@+	-196; 225	SV2B	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.

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	51	0.27%	1.08%	56.04%	34	0.809524
anti	40	0.21%	0.85%	43.96%	29	0.634921
both	91	0.48%	1.93%	100.00%	63	1.44444
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	57	0.27%	1.03%	58.76%	34	0.904762
anti	40	0.19%	0.72%	41.24%	29	0.634921
both	97	0.47%	1.75%	100.00%	63	1.53968

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)
chr4:144257914@+	-1000; 213	GAB1	7; 0	13; 0
chrX:139866722@-	-1000; 96	CDR1	0; 5	0; 5
chr17:39623680@-	-1000; 52	KRT32	0; 3	0; 3
chr14:48143952@-	-1000; 80	MDGA2	3; 0	3; 0
chr12:14133052@-	-1000; 96	GRIN2B	3; 0	3; 0
chr11:62623517@+	-1000; 112	SLC3A2	0; 3	0; 3
chr5:24645086@-	-1000; 192	CDH10	2; 0	2; 0
chr19:55770362@-	-1000; 280	SAPS1	2; 0	2; 0
chr17:4843422@+	-1000; 116	RNF167	0; 2	0; 2
chr16:81040102@+	-1000; 300	CENPN	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)
chr4:144257914@+	-1000; 213	GAB1	7; 0	13; 0
chrX:139866722@-	-1000; 96	CDR1	0; 5	0; 5
chr17:39623680@-	-1000; 52	KRT32	0; 3	0; 3
chr14:48143952@-	-1000; 80	MDGA2	3; 0	3; 0
chr12:14133052@-	-1000; 96	GRIN2B	3; 0	3; 0
chr11:62623517@+	-1000; 112	SLC3A2	0; 3	0; 3
chr5:24645086@-	-1000; 192	CDH10	2; 0	2; 0
chr19:55770362@-	-1000; 280	SAPS1	2; 0	2; 0
chr17:4843422@+	-1000; 116	RNF167	0; 2	0; 2
chr16:81040102@+	-1000; 300	CENPN	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	254	1.34%	5.40%	77.20%	198	1.016
anti	75	0.39%	1.59%	22.80%	52	0.3
both	329	1.73%	6.99%	100.00%	250	1.316
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	256	1.23%	4.62%	75.96%	198	1.024
anti	81	0.39%	1.46%	24.04%	52	0.324
both	337	1.62%	6.09%	100.00%	250	1.348

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)
chr16:67471456@+	-275; 1000	HSD11B2	0; 12	0; 14
chr22:39781593@+	-300; 1000	SYNGR1	5; 0	5; 0
chrX:139865423@-	-158; 1000	CDR1	0; 4	0; 4
chr22:39214455@-	-300; 1000	NPTXR	4; 0	4; 0
chr11:10818591@-	-300; 1000	EIF4G2	4; 0	4; 0
chr7:75956114@-	-300; 1000	YWHAG	3; 0	3; 0
chr7:73007522@-	-300; 1000	MLXIPL	3; 0	3; 0
chr5:32604185@+	-300; 1000	SUB1	3; 0	3; 0
chr2:27600096@-	-156; 1000	ZNF513	0; 3	0; 3
chr2:231743963@+	-300; 1000	ITM2C	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)
chr16:67471456@+	-275; 1000	HSD11B2	0; 12	0; 14
chr22:39781593@+	-300; 1000	SYNGR1	5; 0	5; 0
chrX:139865423@-	-158; 1000	CDR1	0; 4	0; 4
chr22:39214455@-	-300; 1000	NPTXR	4; 0	4; 0
chr16:31000473@+	-300; 1000	HSD3B7	0; 2	0; 4
chr11:10818591@-	-300; 1000	EIF4G2	4; 0	4; 0
chr7:75956114@-	-300; 1000	YWHAG	3; 0	3; 0
chr7:73007522@-	-300; 1000	MLXIPL	3; 0	3; 0
chr5:32604185@+	-300; 1000	SUB1	3; 0	3; 0
chr2:27600096@-	-156; 1000	ZNF513	0; 3	0; 3

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	520	2.73%	11.05%	74.93%	210	1.67203
anti	174	0.91%	3.70%	25.07%	101	0.559486
both	694	3.65%	14.74%	100.00%	311	2.23151
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	920	4.43%	16.61%	81.42%	210	2.9582
anti	210	1.01%	3.79%	18.58%	101	0.675241
both	1130	5.44%	20.40%	100.00%	311	3.63344

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_gl000220:109077@+	-758; 300	18S	103; 0	301; 0
chr1:109642814@+	-1000; 210	snoU2-25	58; 0	146; 0
chrUn_gl000220:113347@+	-585; 300	28S	54; 0	81; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 50	0; 81
chr7:80962916@+	-1000; 115	AC004866.1-ENSG00000239843	8; 0	11; 0
chr4:144257914@+	-1000; 213	GAB1	7; 0	13; 0
chr12:120729705@-	-597; 70	U4-ENSG00000202538	6; 0	8; 0
chrX:139866722@-	-1000; 96	CDR1	0; 5	0; 5
chr2:220455705@-	-1000; 149	7SK-ENSG00000222678	5; 0	6; 0
chr13:97601786@-	-1000; 142	7SK-ENSG00000222472	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)
chrUn_gl000220:109077@+	-758; 300	18S	103; 0	301; 0
chr1:109642814@+	-1000; 210	snoU2-25	58; 0	146; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 50	0; 81
chrUn_gl000220:113347@+	-585; 300	28S	54; 0	81; 0
chr1:8266656@-	-1000; 82	U1-ENSG00000200975	2; 0	16; 0
chr4:144257914@+	-1000; 213	GAB1	7; 0	13; 0
chr7:80962916@+	-1000; 115	AC004866.1-ENSG00000239843	8; 0	11; 0
chrX:100889099@-	-1000; 53	U6-ENSG00000207291	4; 0	10; 0
chr4:140606580@-	-1000; 150	7SK-ENSG00000201533	4; 0	8; 0
chr12:120729705@-	-597; 70	U4-ENSG00000202538	6; 0	8; 0

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	494	2.60%	10.49%	73.73%	305	1.1875
anti	176	0.93%	3.74%	26.27%	112	0.423077
both	670	3.52%	14.23%	100.00%	416	1.61058
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	559	2.69%	10.09%	73.75%	305	1.34375
anti	199	0.96%	3.59%	26.25%	112	0.478365
both	758	3.65%	13.69%	100.00%	416	1.82212

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_gl000220:110946@+	-300; 539	18S	38; 0	46; 0
chrUn_gl000220:118417@+	-300; 1000	28S	25; 0	54; 0
chr11:65271080@+	-300; 1000	MALAT1	21; 0	22; 0
chr1:109643234@+	-210; 1000	snoU2-25	15; 0	22; 0
chrY:10036111@-	-300; 1000	RN18S1	0; 12	0; 16
chr16:67471456@+	-275; 1000	HSD11B2	0; 12	0; 14
chr18:77773065@+	-110; 1000	AC090360.1	11; 0	17; 0
chr4:144257786@-	-255; 1000	AC097658.1	0; 7	0; 13
chrX:108297359@-	-216; 1000	RN28S1	0; 6	0; 8
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	6; 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)
chrUn_gl000220:118417@+	-300; 1000	28S	25; 0	54; 0
chrUn_gl000220:110946@+	-300; 539	18S	38; 0	46; 0
chr11:65271080@+	-300; 1000	MALAT1	21; 0	22; 0
chr1:109643234@+	-210; 1000	snoU2-25	15; 0	22; 0
chr18:77773065@+	-110; 1000	AC090360.1	11; 0	17; 0
chrY:10036111@-	-300; 1000	RN18S1	0; 12	0; 16
chr16:67471456@+	-275; 1000	HSD11B2	0; 12	0; 14
chr4:144257786@-	-255; 1000	AC097658.1	0; 7	0; 13
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	6; 0	11; 0
chrX:108297359@-	-216; 1000	RN28S1	0; 6	0; 8

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	470	2.47%	9.98%	91.26%	355	1.18987
anti	45	0.24%	0.96%	8.74%	40	0.113924
both	515	2.71%	10.94%	100.00%	395	1.3038
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	499	2.40%	9.01%	91.39%	355	1.26329
anti	47	0.23%	0.85%	8.61%	40	0.118987
both	546	2.63%	9.86%	100.00%	395	1.38228

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)
chr11:93454988@+	-142; 100	snoU2-30-ENSG00000199675	10; 0	10; 0
chr9:97055216@+	-216; 37	ZNF169	7; 0	7; 0
chr5:94026903@+	-300; 100	ANKRD32	6; 0	6; 0
chr20:2634908@+	-300; 100	SNORD110	6; 0	9; 0
chr11:85418922@-	-300; 100	SYTL2	6; 0	6; 0
chr2:175216709@-	-300; 100	CIR1	5; 0	5; 0
chr19:613070@+	-300; 100	HCN2	5; 0	5; 0
chr5:179048854@-	-300; 100	HNRNPH1	4; 0	4; 0
chr3:52725453@+	-133; 100	SNORD19-ENSG00000222345	4; 0	4; 0
chr19:12953892@+	-300; 100	MAST1	4; 0	4; 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)
chr11:93454988@+	-142; 100	snoU2-30-ENSG00000199675	10; 0	10; 0
chr20:2634908@+	-300; 100	SNORD110	6; 0	9; 0
chr9:97055216@+	-216; 37	ZNF169	7; 0	7; 0
chr1:235622562@-	-300; 100	B3GALNT2	4; 0	7; 0
chr9:140676322@+	-300; 100	EHMT1	2; 0	6; 0
chr5:94026903@+	-300; 100	ANKRD32	6; 0	6; 0
chr11:85418922@-	-300; 100	SYTL2	6; 0	6; 0
chr2:175216709@-	-300; 100	CIR1	5; 0	5; 0
chr19:613070@+	-300; 100	HCN2	5; 0	5; 0
chr5:179048854@-	-300; 100	HNRNPH1	4; 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.