Input data and parameters
Input
| Analysis date: | Wed Apr 27 20:29:58 CST 2022 |
| BAM file: | /dev/stdin |
| Counting algorithm: | uniquely-mapped-reads |
| GTF file: | /home/bayegy/Databases/transcriptome/references/mmu/GCF_000001635.27_GRCm39_genomic.gtf |
| Number of bases for 5'-3' bias computation: | 100 |
| Number of transcripts for 5'-3' bias computation: | 1,000 |
| Paired-end sequencing: | yes |
| Protocol: | non-strand-specific |
| Sorting performed: | no |
Summary
Reads alignment
| Number of mapped reads (left/right): | 20,030,500 / 19,999,212 |
| Number of aligned pairs (without duplicates): | 18,400,279 |
| Total number of alignments: | 46,209,787 |
| Number of secondary alignments: | 6,180,075 |
| Number of non-unique alignments: | 8,931,065 |
| Aligned to genes: | 32,832,744 |
| Ambiguous alignments: | 259,983 |
| No feature assigned: | 4,185,917 |
| Missing chromosome in annotation: | 78 |
| Not aligned: | 1,009,496 |
| Strand specificity estimation (fwd/rev): | 0.5 / 0.5 |
Reads genomic origin
| Exonic: | 32,832,744 / 88.69% |
| Intronic: | 2,078,444 / 5.61% |
| Intergenic: | 2,107,473 / 5.69% |
| Intronic/intergenic overlapping exon: | 733,524 / 1.98% |
Transcript coverage profile
| 5' bias: | 0.66 |
| 3' bias: | 0.3 |
| 5'-3' bias: | 1.48 |
Junction analysis
| Reads at junctions: | 22,586,187 |
| ACCT | 4.68% |
| AGGT | 4.37% |
| TCCT | 3.43% |
| AGCT | 3.4% |
| ATCT | 3.38% |
| GCCT | 3.07% |
| AGGG | 3.06% |
| AGGA | 3.03% |
| AGGC | 3% |
| CCCT | 2.37% |
| AGAT | 2.11% |
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