Resource
| Id | Histone_ChIP-seq/ENCSR409RGJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR409RGJ [biosample_summary="Homo sapiens neurosphere female embryo (17 weeks) originated from ganglionic eminence" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (17 weeks) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN653MVK|/analyses/ENCAN653MVK/} 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 {ENCFF312QHT|/files/ENCFF312QHT/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF312QHT|/files/ENCFF312QHT/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC2 value of 9.27. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR409RGJ | float |
Histone_ChIP-seq_ENCSR409RGJ |
Histone_ChIP-seq ENCSR409RGJ [biosample_summary="Homo sapiens neurosphere female embryo (17 weeks) originated from ganglionic eminence" and target="H3K4me1"]
|
 |
[1.68, 23.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 208368325 | 6.48% | 200487 |
| chr1 | 20334145 | 8.17% | 18616 |
| chr2 | 16693364 | 6.89% | 16700 |
| chr3 | 13304847 | 6.71% | 13318 |
| chr4 | 8979581 | 4.72% | 9566 |
| chr5 | 11244064 | 6.19% | 11210 |
| chr6 | 11331085 | 6.63% | 11474 |
| chr7 | 10553689 | 6.62% | 10775 |
| chr8 | 9265374 | 6.38% | 9417 |
| chr9 | 9182292 | 6.63% | 8504 |
| chr10 | 10040435 | 7.50% | 9597 |
| chr11 | 12354989 | 9.15% | 11031 |
| chr12 | 9391276 | 7.05% | 9051 |
| chr13 | 5217088 | 4.56% | 5629 |
| chr14 | 7278203 | 6.80% | 6882 |
| chr15 | 7079014 | 6.94% | 6593 |
| chr16 | 7267037 | 8.04% | 6462 |
| chr17 | 10503539 | 12.62% | 8490 |
| chr18 | 4715848 | 5.87% | 4972 |
| chr19 | 6923949 | 11.81% | 5693 |
| chr20 | 5871092 | 9.11% | 5443 |
| chr21 | 1994596 | 4.27% | 2003 |
| chr22 | 4795253 | 9.44% | 4056 |
| chrX | 4047565 | 2.59% | 5005 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 200487 | 190 | 41379 | 1039.31 | 691 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF940QJB.bed.gz | 4.33 MB | 7d5a2fdc558837e4c69f0f76b7551d3e |
| ENCFF940QJB.tabix.bed.gz | 2.04 MB | f12d8b1a77af641e38a7c85ba7d88f5e |
| ENCFF940QJB.tabix.bed.gz.tbi | 455.59 KB | 545d7e911e6b3fd695aba58b84c7b27d |
| genomic_resource.yaml | 2.89 KB | 848bd6616b366a10bf9964a1e287e514 |
| statistics/ |