Input data and parameters
Input
| Analysis date: | Wed Apr 27 19:58:50 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): | 20,241,997 / 19,998,124 |
| Number of aligned pairs (without duplicates): | 18,008,415 |
| Total number of alignments: | 42,822,310 |
| Number of secondary alignments: | 2,582,189 |
| Number of non-unique alignments: | 4,092,794 |
| Aligned to genes: | 34,505,260 |
| Ambiguous alignments: | 309,986 |
| No feature assigned: | 3,914,055 |
| Missing chromosome in annotation: | 215 |
| Not aligned: | 1,384,617 |
| Strand specificity estimation (fwd/rev): | 0.5 / 0.5 |
Reads genomic origin
| Exonic: | 34,505,260 / 89.81% |
| Intronic: | 2,752,361 / 7.16% |
| Intergenic: | 1,161,694 / 3.02% |
| Intronic/intergenic overlapping exon: | 813,128 / 2.12% |
Transcript coverage profile
| 5' bias: | 0.64 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.6 |
Junction analysis
| Reads at junctions: | 21,890,626 |
| AGGT | 4.51% |
| ACCT | 4.42% |
| AGGA | 3.62% |
| AGGG | 3.02% |
| TCCT | 2.93% |
| AGCT | 2.87% |
| CCCT | 2.67% |
| AGAT | 2.58% |
| AGAA | 2.46% |
| ATCT | 2.42% |
| AGGC | 2.39% |
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