Resource
| Id | Histone_ChIP-seq/ENCSR878HPJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR878HPJ [biosample_summary="Homo sapiens SK-N-SH" and target="H4K20me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN458BWT|/analyses/ENCAN458BWT/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF338XFC|/files/ENCFF338XFC/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 22532546 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H4K20me1-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) 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 {ENCFF428NUV|/files/ENCFF428NUV/} processed by ChIP-seq ENCODE4 v1.6.1 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 alignments file {ENCFF428NUV|/files/ENCFF428NUV/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.15. 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 {ENCFF338XFC|/files/ENCFF338XFC/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF338XFC|/files/ENCFF338XFC/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 5.42. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR878HPJ | float |
Histone_ChIP-seq_ENCSR878HPJ |
Histone_ChIP-seq ENCSR878HPJ [biosample_summary="Homo sapiens SK-N-SH" and target="H4K20me1"]
|
 |
[1.49, 31.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 57123621 | 1.78% | 41675 |
| chr1 | 4846755 | 1.95% | 3580 |
| chr2 | 4607009 | 1.90% | 3221 |
| chr3 | 3528669 | 1.78% | 2615 |
| chr4 | 1913047 | 1.01% | 1589 |
| chr5 | 3074455 | 1.69% | 2045 |
| chr6 | 2269713 | 1.33% | 1722 |
| chr7 | 3897865 | 2.45% | 2794 |
| chr8 | 2052875 | 1.41% | 1599 |
| chr9 | 2709758 | 1.96% | 2002 |
| chr10 | 3005711 | 2.25% | 2211 |
| chr11 | 2895322 | 2.14% | 2052 |
| chr12 | 2736497 | 2.05% | 1938 |
| chr13 | 1162659 | 1.02% | 1037 |
| chr14 | 1890518 | 1.77% | 1397 |
| chr15 | 2075522 | 2.04% | 1739 |
| chr16 | 2819452 | 3.12% | 1854 |
| chr17 | 3620711 | 4.35% | 2510 |
| chr18 | 855230 | 1.06% | 673 |
| chr19 | 2437148 | 4.16% | 1682 |
| chr20 | 1733205 | 2.69% | 1119 |
| chr21 | 563343 | 1.21% | 379 |
| chr22 | 1352077 | 2.66% | 1021 |
| chrX | 1076080 | 0.69% | 896 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 41675 | 195 | 80943 | 1370.69 | 733 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF626ZQQ.bed.gz | 982.91 KB | 798384aa23c1d5ac8fe5cadd7212922a |
| ENCFF626ZQQ.tabix.bed.gz | 443.98 KB | 685169cb8307121e847f47b8fd4bd38d |
| ENCFF626ZQQ.tabix.bed.gz.tbi | 94.01 KB | d513be98d23d2880210f7376f56981a6 |
| genomic_resource.yaml | 4.52 KB | 1d6b52703bbaaeed58bfc7b28fc6f726 |
| statistics/ |