Resource
| Id | Histone_ChIP-seq/ENCSR000DQZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DQZ [biosample_summary="Homo sapiens GM12864" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN266OIU|/analyses/ENCAN266OIU/} has in progress subobject document {04498b0f-bd4b-4e24-a565-260ece995ad8|/documents/04498b0f-bd4b-4e24-a565-260ece995ad8/} audit_internal_action: Released analysis {ENCAN266OIU|/analyses/ENCAN266OIU/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_warning: Processed alignments file {ENCFF248PKA|/files/ENCFF248PKA/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 17982711 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 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 {ENCFF248PKA|/files/ENCFF248PKA/} 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 {ENCFF248PKA|/files/ENCFF248PKA/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.84. 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 {ENCFF498KPF|/files/ENCFF498KPF/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF498KPF|/files/ENCFF498KPF/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.24. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DQZ | float |
Histone_ChIP-seq_ENCSR000DQZ |
Histone_ChIP-seq ENCSR000DQZ [biosample_summary="Homo sapiens GM12864" and target="H3K4me3"]
|
 |
[1.87, 77.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 37226756 | 1.16% | 28953 |
| chr1 | 3660597 | 1.47% | 2844 |
| chr2 | 2538721 | 1.05% | 2034 |
| chr3 | 2053932 | 1.04% | 1518 |
| chr4 | 1348333 | 0.71% | 1005 |
| chr5 | 1811641 | 1.00% | 1343 |
| chr6 | 2297685 | 1.35% | 1710 |
| chr7 | 1732665 | 1.09% | 1400 |
| chr8 | 1396296 | 0.96% | 1142 |
| chr9 | 1499086 | 1.08% | 1195 |
| chr10 | 1523996 | 1.14% | 1190 |
| chr11 | 1922180 | 1.42% | 1418 |
| chr12 | 1990797 | 1.49% | 1506 |
| chr13 | 764321 | 0.67% | 629 |
| chr14 | 1287414 | 1.20% | 1021 |
| chr15 | 1233565 | 1.21% | 948 |
| chr16 | 1523506 | 1.69% | 1196 |
| chr17 | 2228640 | 2.68% | 1687 |
| chr18 | 602094 | 0.75% | 489 |
| chr19 | 2436423 | 4.16% | 1935 |
| chr20 | 984766 | 1.53% | 791 |
| chr21 | 376397 | 0.81% | 323 |
| chr22 | 882593 | 1.74% | 680 |
| chrX | 1078590 | 0.69% | 901 |
| chrY | 52518 | 0.09% | 48 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 28953 | 168 | 18425 | 1285.77 | 872 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF704LTU.bed.gz | 756.13 KB | d95440fabbeb28071303826766241a3e |
| ENCFF704LTU.tabix.bed.gz | 332.6 KB | 97246a9822401f79dd56fe9b4a0829b6 |
| ENCFF704LTU.tabix.bed.gz.tbi | 146.67 KB | 02aa253307c080a46e7ffa771adae98d |
| genomic_resource.yaml | 5.03 KB | 4846a3eba5b83917409d07c2842033fc |
| statistics/ |