Input data and parameters
Input
| Analysis date: | Wed Apr 27 20:31:27 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): | 22,924,073 / 22,929,526 |
| Number of aligned pairs (without duplicates): | 21,068,745 |
| Total number of alignments: | 54,245,244 |
| Number of secondary alignments: | 8,391,645 |
| Number of non-unique alignments: | 11,855,082 |
| Aligned to genes: | 37,238,999 |
| Ambiguous alignments: | 295,437 |
| No feature assigned: | 4,855,627 |
| Missing chromosome in annotation: | 99 |
| Not aligned: | 1,245,497 |
| Strand specificity estimation (fwd/rev): | 0.5 / 0.5 |
Reads genomic origin
| Exonic: | 37,238,999 / 88.46% |
| Intronic: | 2,327,913 / 5.53% |
| Intergenic: | 2,527,714 / 6% |
| Intronic/intergenic overlapping exon: | 825,965 / 1.96% |
Transcript coverage profile
| 5' bias: | 0.63 |
| 3' bias: | 0.31 |
| 5'-3' bias: | 1.46 |
Junction analysis
| Reads at junctions: | 25,800,335 |
| ACCT | 4.57% |
| AGGT | 4.22% |
| ATCT | 3.48% |
| AGCT | 3.44% |
| TCCT | 3.29% |
| AGGG | 3.24% |
| AGGC | 3.14% |
| GCCT | 3.02% |
| AGGA | 2.97% |
| CCCT | 2.28% |
| AGAT | 2.09% |
.png)
.png)
.png)
