Parameters
input_file: 20090724_LUjt1_1_hg19_ensembl59_S_iCLIP_TDP-43_Brain-C30_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: 96620
[x-link sites] used in any map: 18638 (19.29%)
[single hits (=G+T), cDNA counts] total: 96620
[single hits (=G+T), cDNA counts] used in any map: 23322 (20.84%)

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	4652	4.81%	24.96%	5121	4.58%	21.96%
intron-exon	-300; 300	5212	5.39%	27.96%	5653	5.05%	24.24%
5-ncRNA	-1000; 300	2170	2.25%	11.64%	4062	3.63%	17.42%
ncRNA-3	-300; 1000	1892	1.96%	10.15%	3185	2.85%	13.66%
ORF-3UTR	-300; 300	1381	1.43%	7.41%	1560	1.39%	6.69%
5UTR-ORF	-300; 300	360	0.37%	1.93%	421	0.38%	1.81%
inter-5UTR	-1000; 300	710	0.73%	3.81%	1012	0.90%	4.34%
3UTR-inter	-300; 1000	1355	1.40%	7.27%	1500	1.34%	6.43%
inter-5	-1000; 300	2120	2.19%	11.37%	3922	3.50%	16.82%
3-inter	-300; 1000	2391	2.47%	12.83%	3128	2.79%	13.41%
BP best in intron	-300; 100	2327	2.41%	12.49%	2546	2.27%	10.92%

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	4340	4.49%	23.29%	93.29%	3380	1.1989
anti	312	0.32%	1.67%	6.71%	244	0.0861878
both	4652	4.81%	24.96%	100.00%	3620	1.28508
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	4772	4.26%	20.46%	93.18%	3380	1.31823
anti	349	0.31%	1.50%	6.82%	244	0.0964088
both	5121	4.58%	21.96%	100.00%	3620	1.41464

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)
chr10:103590823@-	-50; 300	KCNIP2	45; 0	76; 0
chr10:135150336@-	-69; 300	CALY	22; 0	36; 0
chr11:1023507@-	-72; 300	MUC6	0; 21	0; 26
chr1:1158622@-	-57; 300	SDF4	20; 0	22; 0
chr6:167368981@-	-67; 300	RNASET2	19; 0	24; 0
chr17:982568@-	-31; 300	ABR	18; 0	32; 0
chr1:156387702@-	-62; 300	C1orf61	18; 0	21; 0
chr7:139025365@+	-85; 256	C7orf55	17; 0	80; 0
chr21:44269334@-	-300; 300	WDR4	15; 0	17; 0
chr17:7111392@-	-83; 300	DLG4	15; 0	22; 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)
chr7:139025365@+	-85; 256	C7orf55	17; 0	80; 0
chr10:103590823@-	-50; 300	KCNIP2	45; 0	76; 0
chr10:135150336@-	-69; 300	CALY	22; 0	36; 0
chr17:982568@-	-31; 300	ABR	18; 0	32; 0
chr11:1023507@-	-72; 300	MUC6	0; 21	0; 26
chr6:167368981@-	-67; 300	RNASET2	19; 0	24; 0
chr17:7111392@-	-83; 300	DLG4	15; 0	22; 0
chr1:1158622@-	-57; 300	SDF4	20; 0	22; 0
chr1:156387702@-	-62; 300	C1orf61	18; 0	21; 0
chr7:158055898@+	-72; 300	AC019043.2	0; 13	0; 20

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	4908	5.08%	26.33%	94.17%	3947	1.17248
anti	304	0.31%	1.63%	5.83%	248	0.072623
both	5212	5.39%	27.96%	100.00%	4186	1.2451
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	5305	4.74%	22.75%	93.84%	3947	1.26732
anti	348	0.31%	1.49%	6.16%	248	0.0831343
both	5653	5.05%	24.24%	100.00%	4186	1.35045

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)
chr19:4198136@+	-300; 196	ANKRD24	33; 0	46; 0
chr3:9291368@-	-300; 300	SRGAP3	25; 0	42; 0
chr2:127811587@-	-300; 54	BIN1	20; 0	26; 0
chr19:11467477@+	-300; 87	AC024575.1	15; 0	16; 0
chr10:103874722@-	-300; 280	LDB1	14; 0	20; 0
chr7:31117605@+	-300; 54	ADCYAP1R1	13; 0	13; 0
chr20:1165318@-	-231; 300	C20orf46	12; 0	13; 0
chr4:31018439@-	-300; 44	AC110766.1	0; 11	0; 13
chr20:10286776@+	-300; 300	SNAP25	11; 0	11; 0
chr2:47387942@-	-300; 300	CALM2	11; 0	15; 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)
chr19:4198136@+	-300; 196	ANKRD24	33; 0	46; 0
chr3:9291368@-	-300; 300	SRGAP3	25; 0	42; 0
chr2:127811587@-	-300; 54	BIN1	20; 0	26; 0
chr10:103874722@-	-300; 280	LDB1	14; 0	20; 0
chr11:18425240@+	-300; 59	LDHA	3; 0	17; 0
chr19:11467477@+	-300; 87	AC024575.1	15; 0	16; 0
chr2:47387942@-	-300; 300	CALM2	11; 0	15; 0
chr10:103589698@-	-241; 49	KCNIP2	11; 0	15; 0
chr1:182356426@-	-300; 259	GLUL	1; 1	1; 14
chr22:39715115@-	-130; 42	RPL3	7; 0	14; 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	1452	1.50%	7.79%	66.91%	586	1.40154
anti	718	0.74%	3.85%	33.09%	460	0.69305
both	2170	2.25%	11.64%	100.00%	1036	2.09459
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	3184	2.84%	13.65%	78.39%	586	3.07336
anti	878	0.78%	3.76%	21.61%	460	0.84749
both	4062	3.63%	17.42%	100.00%	1036	3.92085

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)
chr1:109642814@+	-1000; 210	snoU2-25	124; 0	879; 0
chrUn_gl000220:109077@+	-758; 300	18S	89; 0	183; 0
chrUn_gl000220:113347@+	-585; 300	28S	86; 0	195; 0
chr9:138900081@+	-1000; 300	AL355574.1	0; 54	0; 90
chr11:65269806@+	-1000; 29	MALAT1	52; 0	66; 0
chr14:101318726@+	-1000; 49	MEG3, hsa-mir-770	49; 0	59; 0
chr3:160233023@-	-108; 165	KPNA4, snoU90	42; 0	125; 0
chr1:241469181@-	-1000; 152	RGS7, RP11-306K13.1	41; 0	62; 0
chrM:16022@-	-274; 34	J01415.14	19; 2	137; 2
chr1:159172176@-	-1000; 69	CTA-134P22.2	0; 20	0; 24

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)
chr1:109642814@+	-1000; 210	snoU2-25	124; 0	879; 0
chrUn_gl000220:113347@+	-585; 300	28S	86; 0	195; 0
chrUn_gl000220:109077@+	-758; 300	18S	89; 0	183; 0
chrM:16022@-	-274; 34	J01415.14	19; 2	137; 2
chr3:160233023@-	-108; 165	KPNA4, snoU90	42; 0	125; 0
chr9:138900081@+	-1000; 300	AL355574.1	0; 54	0; 90
chr2:27273131@-	-1000; 42	AC013472.6	0; 14	0; 82
chr11:65269806@+	-1000; 29	MALAT1	52; 0	66; 0
chr1:241469181@-	-1000; 152	RGS7, RP11-306K13.1	41; 0	62; 0
chr14:101318726@+	-1000; 49	MEG3, hsa-mir-770	49; 0	59; 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	1267	1.31%	6.80%	66.97%	526	1.45465
anti	625	0.65%	3.35%	33.03%	351	0.717566
both	1892	1.96%	10.15%	100.00%	871	2.17222
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	2316	2.07%	9.93%	72.72%	526	2.65901
anti	869	0.78%	3.73%	27.28%	351	0.997704
both	3185	2.85%	13.66%	100.00%	871	3.65672

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	107; 0	145; 0
chrUn_gl000220:110946@+	-300; 539	18S	99; 0	342; 0
chrUn_gl000220:118417@+	-300; 1000	28S	69; 0	250; 0
chr3:160232693@-	-165; 362	KPNA4, snoU90	37; 0	51; 0
chr14:101323580@-	-300; 1000	AL117190.1-ENSG00000214512	0; 35	0; 49
chrM:15953@+	-33; 309	J01415.6	8; 20	41; 126
chr14:101318824@+	-49; 1000	MEG3, hsa-mir-770	24; 0	26; 0
chr11:62609089@-	-96; 978	U2-ENSG00000222328	23; 0	36; 0
chr1:109643234@+	-210; 1000	snoU2-25	22; 0	43; 0
chrM:15954@-	-34; 606	J01415.14	12; 9	57; 67

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_gl000220:110946@+	-300; 539	18S	99; 0	342; 0
chrUn_gl000220:118417@+	-300; 1000	28S	69; 0	250; 0
chrM:15953@+	-33; 309	J01415.6	8; 20	41; 126
chr11:65271080@+	-300; 1000	MALAT1	107; 0	145; 0
chrM:15954@-	-34; 606	J01415.14	12; 9	57; 67
chr22:43011399@+	-75; 1000	U12-ENSG00000199382	14; 0	95; 0
chr7:148638658@+	-40; 1000	Y_RNA-ENSG00000252310	10; 0	70; 0
chr3:160232693@-	-165; 362	KPNA4, snoU90	37; 0	51; 0
chr14:101323580@-	-300; 1000	AL117190.1-ENSG00000214512	0; 35	0; 49
chr1:109643234@+	-210; 1000	snoU2-25	22; 0	43; 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	1343	1.39%	7.21%	97.25%	863	1.50392
anti	38	0.04%	0.20%	2.75%	32	0.0425532
both	1381	1.43%	7.41%	100.00%	893	1.54647
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	1514	1.35%	6.49%	97.05%	863	1.69541
anti	46	0.04%	0.20%	2.95%	32	0.0515118
both	1560	1.39%	6.69%	100.00%	893	1.74692

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)
chr10:73822514@-	-74; 300	SPOCK2	44; 0	87; 0
chr16:67472427@-	-82; 253	ATP6V0D1	22; 0	39; 0
chr10:22825820@-	-195; 300	PIP5K2A	21; 0	27; 0
chr5:73925375@-	-221; 300	ENC1	19; 0	23; 0
chr11:35275966@-	-194; 300	SLC1A2	15; 0	16; 0
chr1:41092185@-	-108; 300	RIMS3	12; 0	14; 0
chr1:20809678@-	-267; 300	CAMK2N1	10; 0	11; 0
chr3:5025377@+	-300; 300	BHLHE40	9; 0	16; 0
chr2:55199719@-	-300; 198	RTN4	9; 0	10; 0
chr16:23478907@-	-57; 300	GGA2	9; 0	15; 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)
chr10:73822514@-	-74; 300	SPOCK2	44; 0	87; 0
chr16:67472427@-	-82; 253	ATP6V0D1	22; 0	39; 0
chr10:22825820@-	-195; 300	PIP5K2A	21; 0	27; 0
chr5:73925375@-	-221; 300	ENC1	19; 0	23; 0
chr3:5025377@+	-300; 300	BHLHE40	9; 0	16; 0
chr11:35275966@-	-194; 300	SLC1A2	15; 0	16; 0
chr16:23478907@-	-57; 300	GGA2	9; 0	15; 0
chr1:41092185@-	-108; 300	RIMS3	12; 0	14; 0
chr5:58147354@+	-182; 300	RAB3C	8; 0	11; 0
chr1:20809678@-	-267; 300	CAMK2N1	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	335	0.35%	1.80%	93.06%	219	1.39583
anti	25	0.03%	0.13%	6.94%	23	0.104167
both	360	0.37%	1.93%	100.00%	240	1.5
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	395	0.35%	1.69%	93.82%	219	1.64583
anti	26	0.02%	0.11%	6.18%	23	0.108333
both	421	0.38%	1.81%	100.00%	240	1.75417

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)
chr4:158141875@+	-70; 203	GRIA2	25; 0	36; 0
chr4:71588290@+	-290; 89	RUFY3	18; 0	27; 0
chr2:61764828@-	-277; 66	XPO1	15; 0	23; 0
chr12:121093613@+	-256; 231	CABP1	11; 0	18; 0
chr6:31508971@-	-66; 265	BAT1	8; 0	15; 0
chr18:35145603@-	-198; 143	CELF4	5; 0	5; 0
chr5:86564268@+	-282; 269	RASA1	4; 0	4; 0
chr17:47755471@-	-62; 89	SPOP	4; 0	5; 0
chr11:66115015@-	-73; 300	AP001107.2	4; 0	5; 0
chrX:139866530@-	-96; 300	CDR1	0; 3	0; 3

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)
chr4:158141875@+	-70; 203	GRIA2	25; 0	36; 0
chr4:71588290@+	-290; 89	RUFY3	18; 0	27; 0
chr2:61764828@-	-277; 66	XPO1	15; 0	23; 0
chr12:121093613@+	-256; 231	CABP1	11; 0	18; 0
chr6:31508971@-	-66; 265	BAT1	8; 0	15; 0
chr7:91763677@-	-83; 96	CYP51A1	3; 0	5; 0
chr18:35145603@-	-198; 143	CELF4	5; 0	5; 0
chr17:47755471@-	-62; 89	SPOP	4; 0	5; 0
chr11:66115015@-	-73; 300	AP001107.2	4; 0	5; 0
chr5:86564268@+	-282; 269	RASA1	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 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	424	0.44%	2.27%	59.72%	219	1.1013
anti	286	0.30%	1.53%	40.28%	166	0.742857
both	710	0.73%	3.81%	100.00%	385	1.84416
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	534	0.48%	2.29%	52.77%	219	1.38701
anti	478	0.43%	2.05%	47.23%	166	1.24156
both	1012	0.90%	4.34%	100.00%	385	2.62857

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)
chr6:40555203@-	-1000; 262	LRFN2	27; 0	34; 0
chr15:80737492@-	-1000; 74	AC016705.1	0; 26	0; 33
chr14:65569226@-	-1000; 85	MAX	26; 0	41; 0
chr13:26828275@+	-1000; 251	CDK8	26; 0	67; 0
chr14:48143952@-	-1000; 80	MDGA2	22; 0	30; 0
chr12:122459860@+	-1000; 68	BCL7A	19; 0	29; 0
chr4:144257914@+	-1000; 213	GAB1	13; 0	14; 0
chr13:41635409@+	-1000; 200	WBP4	0; 11	0; 54
chr21:38445469@-	-1000; 90	PIGP	0; 9	0; 9
chr19:36705503@+	-1000; 297	ZNF146	0; 9	0; 11

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)
chr15:89878025@-	-1000; 61	POLG	0; 9	0; 71
chr13:26828275@+	-1000; 251	CDK8	26; 0	67; 0
chr13:41635409@+	-1000; 200	WBP4	0; 11	0; 54
chr14:65569226@-	-1000; 85	MAX	26; 0	41; 0
chr11:66115160@-	-1000; 72	AP001107.2	0; 7	0; 39
chr6:40555203@-	-1000; 262	LRFN2	27; 0	34; 0
chr15:80737492@-	-1000; 74	AC016705.1	0; 26	0; 33
chr14:48143952@-	-1000; 80	MDGA2	22; 0	30; 0
chr12:122459860@+	-1000; 68	BCL7A	19; 0	29; 0
chr17:37026255@+	-1000; 93	LASP1	0; 3	0; 22

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	1115	1.15%	5.98%	82.29%	772	1.18997
anti	240	0.25%	1.29%	17.71%	175	0.256137
both	1355	1.40%	7.27%	100.00%	937	1.4461
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	1225	1.09%	5.25%	81.67%	772	1.30736
anti	275	0.25%	1.18%	18.33%	175	0.29349
both	1500	1.34%	6.43%	100.00%	937	1.60085

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; 21	0; 38
chr3:9543479@-	-206; 1000	LHFPL4	20; 0	23; 0
chr22:39781593@+	-300; 1000	SYNGR1	16; 0	24; 0
chr22:39214455@-	-300; 1000	NPTXR	13; 0	16; 0
chr11:35272751@-	-300; 1000	SLC1A2	13; 0	13; 0
chr12:7311526@+	-300; 1000	CLSTN3	12; 0	15; 0
chr7:30199534@+	-192; 1000	C7orf41	9; 0	13; 0
chr7:102740021@-	-100; 1000	NAPEPLD	0; 7	0; 13
chr6:43149243@+	-300; 334	SRF	7; 0	7; 0
chr5:71502853@+	-300; 1000	MAP1B	7; 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)
chr16:67471456@+	-275; 1000	HSD11B2	0; 21	0; 38
chr22:39781593@+	-300; 1000	SYNGR1	16; 0	24; 0
chr3:9543479@-	-206; 1000	LHFPL4	20; 0	23; 0
chr22:39214455@-	-300; 1000	NPTXR	13; 0	16; 0
chr12:7311526@+	-300; 1000	CLSTN3	12; 0	15; 0
chr7:102740021@-	-100; 1000	NAPEPLD	0; 7	0; 13
chr7:30199534@+	-192; 1000	C7orf41	9; 0	13; 0
chr11:35272751@-	-300; 1000	SLC1A2	13; 0	13; 0
chr18:72102961@-	-300; 1000	FAM69C	7; 0	11; 0
chr17:8024297@-	-294; 1000	HES7	4; 3	7; 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	1121	1.16%	6.01%	52.88%	478	1.09259
anti	999	1.03%	5.36%	47.12%	553	0.973684
both	2120	2.19%	11.37%	100.00%	1026	2.06628
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	2391	2.14%	10.25%	60.96%	478	2.33041
anti	1531	1.37%	6.56%	39.04%	553	1.4922
both	3922	3.50%	16.82%	100.00%	1026	3.82261

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)
chr1:109642814@+	-1000; 210	snoU2-25	124; 0	879; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 121	0; 351
chrUn_gl000220:109077@+	-758; 300	18S	89; 0	183; 0
chrUn_gl000220:113347@+	-585; 300	28S	86; 0	195; 0
chr9:138900081@+	-1000; 300	AL355574.1	0; 54	0; 90
chr6:40555203@-	-1000; 262	LRFN2	27; 0	34; 0
chr15:80737492@-	-1000; 74	AC016705.1	0; 26	0; 33
chr14:65569226@-	-1000; 85	MAX	26; 0	41; 0
chr13:26828275@+	-1000; 251	CDK8	26; 0	67; 0
chr14:48143952@-	-1000; 80	MDGA2	22; 0	30; 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)
chr1:109642814@+	-1000; 210	snoU2-25	124; 0	879; 0
chrUn_gl000220:117814@-	-1000; 67	AL592188.5	0; 121	0; 351
chrUn_gl000220:113347@+	-585; 300	28S	86; 0	195; 0
chrUn_gl000220:109077@+	-758; 300	18S	89; 0	183; 0
chr9:138900081@+	-1000; 300	AL355574.1	0; 54	0; 90
chr15:89878025@-	-1000; 61	POLG	0; 9	0; 71
chr13:26828275@+	-1000; 251	CDK8	26; 0	67; 0
chr13:41635409@+	-1000; 200	WBP4	0; 11	0; 54
chrM:5903@+	-162; 300	J01415.8	5; 7	5; 47
chr14:65569226@-	-1000; 85	MAX	26; 0	41; 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	1700	1.76%	9.12%	71.10%	977	1.21602
anti	691	0.72%	3.71%	28.90%	437	0.494278
both	2391	2.47%	12.83%	100.00%	1398	1.7103
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	2356	2.11%	10.10%	75.32%	977	1.68526
anti	772	0.69%	3.31%	24.68%	437	0.552217
both	3128	2.79%	13.41%	100.00%	1398	2.23748

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	107; 0	145; 0
chrUn_gl000220:110946@+	-300; 539	18S	99; 0	342; 0
chrUn_gl000220:118417@+	-300; 1000	28S	69; 0	250; 0
chr14:101323580@-	-300; 1000	AL117190.1-ENSG00000214512	0; 35	0; 49
chr1:109643234@+	-210; 1000	snoU2-25	22; 0	43; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 21	0; 38
chr3:9543479@-	-206; 1000	LHFPL4	20; 0	23; 0
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	19; 0	31; 0
chr10:133994727@-	-160; 1000	RP11-140A10.3	0; 17	0; 18
chr22:39781593@+	-300; 1000	SYNGR1	16; 0	24; 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_gl000220:110946@+	-300; 539	18S	99; 0	342; 0
chrUn_gl000220:118417@+	-300; 1000	28S	69; 0	250; 0
chr11:65271080@+	-300; 1000	MALAT1	107; 0	145; 0
chr14:101323580@-	-300; 1000	AL117190.1-ENSG00000214512	0; 35	0; 49
chr1:109643234@+	-210; 1000	snoU2-25	22; 0	43; 0
chr16:67471456@+	-275; 1000	HSD11B2	0; 21	0; 38
chr6:52860748@+	-166; 1000	7SK-ENSG00000202198	19; 0	31; 0
chr22:39781593@+	-300; 1000	SYNGR1	16; 0	24; 0
chr3:9543479@-	-206; 1000	LHFPL4	20; 0	23; 0
chr10:133994727@-	-160; 1000	RP11-140A10.3	0; 17	0; 18

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	2128	2.20%	11.42%	91.45%	1589	1.20498
anti	199	0.21%	1.07%	8.55%	179	0.112684
both	2327	2.41%	12.49%	100.00%	1766	1.31767
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	2326	2.08%	9.97%	91.36%	1589	1.3171
anti	220	0.20%	0.94%	8.64%	179	0.124575
both	2546	2.27%	10.92%	100.00%	1766	1.44168

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	21; 0	48; 0
chr2:127811623@-	-300; 36	BIN1	20; 0	26; 0
chr19:2337060@+	-300; 100	AC004410.1	16; 0	17; 0
chr7:31117581@+	-300; 22	ADCYAP1R1	15; 0	15; 0
chr12:113566108@-	-300; 100	RASAL1	14; 0	16; 0
chr17:30354693@+	-300; 92	LRRC37B	12; 0	13; 0
chr12:121093851@+	-300; 42	CABP1	12; 0	19; 0
chr19:11467032@+	-172; 100	AC024575.1	11; 0	12; 0
chr17:7107644@-	-300; 74	DLG4	11; 0	15; 0
chr12:52446230@+	-300; 47	NR4A1	11; 0	11; 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	21; 0	48; 0
chr2:127811623@-	-300; 36	BIN1	20; 0	26; 0
chr12:121093851@+	-300; 42	CABP1	12; 0	19; 0
chr19:2337060@+	-300; 100	AC004410.1	16; 0	17; 0
chr12:113566108@-	-300; 100	RASAL1	14; 0	16; 0
chr7:31117581@+	-300; 22	ADCYAP1R1	15; 0	15; 0
chr17:7107644@-	-300; 74	DLG4	11; 0	15; 0
chr17:30354693@+	-300; 92	LRRC37B	12; 0	13; 0
chr19:11467032@+	-172; 100	AC024575.1	11; 0	12; 0
chr10:88649475@+	-300; 100	U1-ENSG00000200176	2; 0	12; 0

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