Resource
| Id | Histone_ChIP-seq/ENCSR508UPW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR508UPW [biosample_summary="Homo sapiens esophagus squamous epithelium tissue female adult (53 years)" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female adult (53 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN945CIO|/analyses/ENCAN945CIO/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN945CIO|/analyses/ENCAN945CIO/} has in progress subobject document {69649674-9409-432b-829f-8a1a555f0dd8|/documents/69649674-9409-432b-829f-8a1a555f0dd8/} audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.8 is acceptable. ENCODE processed alignments file {ENCFF117IKR|/files/ENCFF117IKR/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.82. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed alignments file {ENCFF117IKR|/files/ENCFF117IKR/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 5.94. audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.8 is acceptable. ENCODE processed alignments file {ENCFF088NXG|/files/ENCFF088NXG/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.88. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed alignments file {ENCFF088NXG|/files/ENCFF088NXG/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.79. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR508UPW | float |
Histone_ChIP-seq_ENCSR508UPW |
Histone_ChIP-seq ENCSR508UPW [biosample_summary="Homo sapiens esophagus squamous epithelium tissue female adult (53 years)" and target="H3K4me3"]
|
 |
[1.53, 93] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 62784357 | 1.95% | 41125 |
| chr1 | 6318940 | 2.54% | 4003 |
| chr2 | 4312260 | 1.78% | 2870 |
| chr3 | 3484522 | 1.76% | 2287 |
| chr4 | 2535821 | 1.33% | 1687 |
| chr5 | 2936939 | 1.62% | 1935 |
| chr6 | 3533099 | 2.07% | 2326 |
| chr7 | 3052050 | 1.92% | 2037 |
| chr8 | 2326914 | 1.60% | 1576 |
| chr9 | 2719542 | 1.97% | 1832 |
| chr10 | 2760501 | 2.06% | 1950 |
| chr11 | 3331741 | 2.47% | 2013 |
| chr12 | 3299299 | 2.48% | 2078 |
| chr13 | 1295259 | 1.13% | 910 |
| chr14 | 2008507 | 1.88% | 1272 |
| chr15 | 2028872 | 1.99% | 1307 |
| chr16 | 2466685 | 2.73% | 1666 |
| chr17 | 3674958 | 4.41% | 2271 |
| chr18 | 1078672 | 1.34% | 772 |
| chr19 | 4061342 | 6.93% | 2725 |
| chr20 | 1670588 | 2.59% | 1072 |
| chr21 | 694755 | 1.49% | 511 |
| chr22 | 1452661 | 2.86% | 939 |
| chrX | 1740430 | 1.12% | 1086 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 41125 | 195 | 25852 | 1526.67 | 998 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF313UUQ.bed.gz | 1.07 MB | b92ba909e216aaaf6e7b6183c4276bd4 |
| ENCFF313UUQ.tabix.bed.gz | 469.86 KB | afb53469c8c458df22a6a21261a9d432 |
| ENCFF313UUQ.tabix.bed.gz.tbi | 217.77 KB | d7e1a121e35ee5918a2d0a71720acfc3 |
| genomic_resource.yaml | 4.32 KB | d798b14fc30c1a9ec8213691491379aa |
| statistics/ |