Resource
| Id | Histone_ChIP-seq/ENCSR344TLI |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR344TLI [biosample_summary="Homo sapiens right lobe of liver tissue female adult (53 years)" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female adult (53 years) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN357LTK|/analyses/ENCAN357LTK/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF188KCU|/files/ENCFF188KCU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 17368420 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 {ENCFF188KCU|/files/ENCFF188KCU/} processed by ChIP-seq ENCODE3 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 {ENCFF188KCU|/files/ENCFF188KCU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.51. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR344TLI | float |
Histone_ChIP-seq_ENCSR344TLI |
Histone_ChIP-seq ENCSR344TLI [biosample_summary="Homo sapiens right lobe of liver tissue female adult (53 years)" and target="H3K4me3"]
|
 |
[1.24, 57.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 51926998 | 1.61% | 39199 |
| chr1 | 5134512 | 2.06% | 3836 |
| chr1_KI270712v1_random | 2774 | 1.58% | 5 |
| chr1_KI270713v1_random | 1428 | 3.50% | 4 |
| chr2 | 3644440 | 1.50% | 2760 |
| chr2_KI270716v1_random | 283 | 0.18% | 1 |
| chr3 | 2988362 | 1.51% | 2194 |
| chr4 | 2290847 | 1.20% | 1797 |
| chr4_GL000008v2_random | 587 | 0.28% | 1 |
| chr5 | 2447046 | 1.35% | 1856 |
| chr6 | 2946557 | 1.73% | 2240 |
| chr7 | 2531160 | 1.59% | 1975 |
| chr8 | 1935171 | 1.33% | 1480 |
| chr9 | 2221716 | 1.61% | 1711 |
| chr9_KI270717v1_random | 957 | 2.39% | 1 |
| chr10 | 2262694 | 1.69% | 1734 |
| chr11 | 2748075 | 2.03% | 1897 |
| chr12 | 2727743 | 2.05% | 2031 |
| chr13 | 1131540 | 0.99% | 929 |
| chr14 | 1683979 | 1.57% | 1204 |
| chr14_GL000009v2_random | 364 | 0.18% | 1 |
| chr15 | 1611718 | 1.58% | 1221 |
| chr16 | 2019848 | 2.24% | 1511 |
| chr17 | 2847117 | 3.42% | 1992 |
| chr17_GL000205v2_random | 3599 | 1.94% | 4 |
| chr17_KI270729v1_random | 3249 | 1.16% | 6 |
| chr18 | 949083 | 1.18% | 742 |
| chr19 | 3303673 | 5.64% | 2661 |
| chr20 | 1323877 | 2.05% | 1005 |
| chr21 | 528290 | 1.13% | 420 |
| chr22 | 1169278 | 2.30% | 872 |
| chr22_KI270733v1_random | 840 | 0.47% | 3 |
| chr22_KI270736v1_random | 849 | 0.47% | 2 |
| chrUn_GL000195v1 | 2091 | 1.14% | 4 |
| chrUn_GL000216v2 | 631 | 0.36% | 1 |
| chrUn_GL000218v1 | 278 | 0.17% | 1 |
| chrUn_GL000219v1 | 5816 | 3.25% | 5 |
| chrUn_GL000220v1 | 591 | 0.37% | 2 |
| chrUn_KI270336v1 | 274 | 26.71% | 1 |
| chrUn_KI270435v1 | 577 | 0.62% | 2 |
| chrUn_KI270438v1 | 2826 | 2.51% | 6 |
| chrUn_KI270442v1 | 664 | 0.17% | 1 |
| chrUn_KI270467v1 | 638 | 16.28% | 1 |
| chrUn_KI270589v1 | 206 | 0.46% | 1 |
| chrUn_KI270757v1 | 223 | 0.31% | 1 |
| chrX | 1450527 | 0.93% | 1077 |
| 3321 contigs with no values (183074440 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 39199 | 200 | 12545 | 1324.7 | 870 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF636VXP.bed.gz | 999.65 KB | c5a214849f80c88c4d5f7ab2dca2f44d |
| ENCFF636VXP.tabix.bed.gz | 440.37 KB | 303091aa0651e39da09f274d30db9848 |
| ENCFF636VXP.tabix.bed.gz.tbi | 207.39 KB | b9bd0b3172d4d7743929e3bed848420d |
| genomic_resource.yaml | 3.26 KB | ad88863ca8171472b9cace2e0fe56bd9 |
| statistics/ |