Resource
| Id | Histone_ChIP-seq/ENCSR575ICR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR575ICR [biosample_summary="Homo sapiens germinal matrix tissue male embryo (20 weeks)" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (20 weeks) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN504BLY|/analyses/ENCAN504BLY/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} 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 redacted alignments file {ENCFF859CZR|/files/ENCFF859CZR/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.83. 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 redacted alignments file {ENCFF859CZR|/files/ENCFF859CZR/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC2 value of 5.95. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR575ICR | float |
Histone_ChIP-seq_ENCSR575ICR |
Histone_ChIP-seq ENCSR575ICR [biosample_summary="Homo sapiens germinal matrix tissue male embryo (20 weeks)" and target="H3K4me3"]
|
 |
[1.98, 99.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 51210274 | 1.59% | 33311 |
| chr1 | 5029800 | 2.02% | 3310 |
| chr2 | 3583760 | 1.48% | 2334 |
| chr3 | 2794738 | 1.41% | 1734 |
| chr4 | 1904949 | 1.00% | 1181 |
| chr5 | 2447314 | 1.35% | 1571 |
| chr6 | 2848684 | 1.67% | 1809 |
| chr7 | 2486914 | 1.56% | 1654 |
| chr8 | 1909503 | 1.32% | 1220 |
| chr9 | 2122411 | 1.53% | 1468 |
| chr10 | 2043818 | 1.53% | 1384 |
| chr11 | 2818121 | 2.09% | 1835 |
| chr12 | 2642469 | 1.98% | 1612 |
| chr13 | 1067052 | 0.93% | 687 |
| chr14 | 1749634 | 1.63% | 1114 |
| chr15 | 1676702 | 1.64% | 1129 |
| chr16 | 2067673 | 2.29% | 1392 |
| chr17 | 2986636 | 3.59% | 1941 |
| chr18 | 938578 | 1.17% | 643 |
| chr19 | 3316743 | 5.66% | 2145 |
| chr20 | 1411080 | 2.19% | 943 |
| chr21 | 456016 | 0.98% | 330 |
| chr22 | 1204682 | 2.37% | 837 |
| chrX | 1647658 | 1.06% | 1011 |
| chrY | 55339 | 0.10% | 27 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 33311 | 180 | 36651 | 1537.34 | 1149 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF765ESV.bed.gz | 759.29 KB | dd8c2ca1a50d3cd4ab3e3e1c7385b287 |
| ENCFF765ESV.tabix.bed.gz | 355.73 KB | 5354ba9d0e7346785beb8a1da8ee093e |
| ENCFF765ESV.tabix.bed.gz.tbi | 183.77 KB | af1260cf04bcc3857e586cf3de25d11d |
| genomic_resource.yaml | 2.8 KB | 0482e3a4c1e4cd801fed3ec17f0c0e81 |
| statistics/ |