Input data and parameters
Input
| Analysis date: | Wed Apr 27 20:14:24 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): | 20,131,787 / 20,097,847 |
| Number of aligned pairs (without duplicates): | 18,594,499 |
| Total number of alignments: | 47,792,822 |
| Number of secondary alignments: | 7,563,188 |
| Number of non-unique alignments: | 10,793,565 |
| Aligned to genes: | 32,192,089 |
| Ambiguous alignments: | 272,327 |
| No feature assigned: | 4,534,745 |
| Missing chromosome in annotation: | 96 |
| Not aligned: | 1,110,620 |
| Strand specificity estimation (fwd/rev): | 0.5 / 0.5 |
Reads genomic origin
| Exonic: | 32,192,089 / 87.65% |
| Intronic: | 1,946,110 / 5.3% |
| Intergenic: | 2,588,635 / 7.05% |
| Intronic/intergenic overlapping exon: | 717,075 / 1.95% |
Transcript coverage profile
| 5' bias: | 0.56 |
| 3' bias: | 0.38 |
| 5'-3' bias: | 1.41 |
Junction analysis
| Reads at junctions: | 21,419,511 |
| ACCT | 4.53% |
| AGGT | 4.13% |
| ATCT | 3.63% |
| AGGG | 3.55% |
| AGGC | 3.42% |
| TCCT | 3.39% |
| AGCT | 3.28% |
| GCCT | 3.18% |
| AGGA | 3% |
| CCCT | 2.34% |
| GCCA | 2.12% |
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