Resource
| Id | Histone_ChIP-seq/ENCSR979RHZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR979RHZ [biosample_summary="Homo sapiens common myeloid progenitor, CD34-positive" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN010KXM|/analyses/ENCAN010KXM/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN010KXM|/analyses/ENCAN010KXM/} has in progress subobject document {b9fd6f16-ddd6-410f-8636-22ac22b05fc9|/documents/b9fd6f16-ddd6-410f-8636-22ac22b05fc9/} audit_not_compliant: Processed unfiltered alignments file {ENCFF361ZXB|/files/ENCFF361ZXB/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 27282117 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_not_compliant: Processed unfiltered alignments file {ENCFF050OLR|/files/ENCFF050OLR/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 12909658 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. 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 {ENCFF622QVA|/files/ENCFF622QVA/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF622QVA|/files/ENCFF622QVA/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.30. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR979RHZ | float |
Histone_ChIP-seq_ENCSR979RHZ |
Histone_ChIP-seq ENCSR979RHZ [biosample_summary="Homo sapiens common myeloid progenitor, CD34-positive" and target="H3K9me3"]
|
 |
[1.94, 17.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 26990036 | 0.84% | 58284 |
| chr1 | 1840854 | 0.74% | 4164 |
| chr2 | 1854518 | 0.77% | 4296 |
| chr3 | 1448952 | 0.73% | 3376 |
| chr4 | 1341255 | 0.71% | 3040 |
| chr5 | 1484237 | 0.82% | 3300 |
| chr6 | 1310820 | 0.77% | 3165 |
| chr7 | 1743834 | 1.09% | 3832 |
| chr8 | 1371166 | 0.94% | 2950 |
| chr9 | 934613 | 0.68% | 2070 |
| chr10 | 1108811 | 0.83% | 2574 |
| chr11 | 897992 | 0.66% | 2151 |
| chr12 | 1388513 | 1.04% | 2909 |
| chr13 | 716509 | 0.63% | 1712 |
| chr14 | 716301 | 0.67% | 1659 |
| chr15 | 804360 | 0.79% | 1801 |
| chr16 | 839435 | 0.93% | 1696 |
| chr17 | 687713 | 0.83% | 1498 |
| chr18 | 520480 | 0.65% | 1206 |
| chr19 | 4127654 | 7.04% | 6561 |
| chr20 | 521504 | 0.81% | 1202 |
| chr21 | 530687 | 1.14% | 1194 |
| chr22 | 390932 | 0.77% | 827 |
| chrX | 391144 | 0.25% | 1045 |
| chrY | 17752 | 0.03% | 56 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 58284 | 133 | 30546 | 463.08 | 352 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF658SDA.bed.gz | 1.08 MB | 4394ae2dbfb355a046190335dd195737 |
| ENCFF658SDA.tabix.bed.gz | 558.2 KB | b3641c53a90e61dfdd31b2fec9194fda |
| ENCFF658SDA.tabix.bed.gz.tbi | 230.47 KB | e2640e9fbf631771fe0a405f5f88f7b2 |
| genomic_resource.yaml | 4.11 KB | 9cf5fe59fb82448c516ebaabd182a7a6 |
| statistics/ |