Input data and parameters
Input
| Analysis date: | Wed Apr 27 19:34:31 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): | 19,826,623 / 19,574,453 |
| Number of aligned pairs (without duplicates): | 18,224,337 |
| Total number of alignments: | 42,678,299 |
| Number of secondary alignments: | 3,277,223 |
| Number of non-unique alignments: | 5,039,281 |
| Aligned to genes: | 33,721,525 |
| Ambiguous alignments: | 439,997 |
| No feature assigned: | 3,477,027 |
| Missing chromosome in annotation: | 469 |
| Not aligned: | 2,299,220 |
| Strand specificity estimation (fwd/rev): | 0.5 / 0.5 |
Reads genomic origin
| Exonic: | 33,721,525 / 90.65% |
| Intronic: | 2,312,544 / 6.22% |
| Intergenic: | 1,164,483 / 3.13% |
| Intronic/intergenic overlapping exon: | 885,091 / 2.38% |
Transcript coverage profile
| 5' bias: | 0.42 |
| 3' bias: | 0.33 |
| 5'-3' bias: | 1.53 |
Junction analysis
| Reads at junctions: | 18,557,074 |
| AGGT | 4.77% |
| ACCT | 4.16% |
| AGGA | 3.42% |
| CCCT | 3.32% |
| AGAA | 3.16% |
| TCCT | 3% |
| AGGG | 2.66% |
| AGAT | 2.57% |
| GCCT | 2.49% |
| AGCT | 2.47% |
| AGGC | 2.29% |
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