Input data and parameters
Input
| Analysis date: | Sun Oct 29 11:39:06 GMT 2023 |
| BAM file: | SRX7354123.markdup.sorted.bam |
| Counting algorithm: | uniquely-mapped-reads |
| GTF file: | gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.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: | strand-specific-reverse |
| Sorting performed: | yes |
Summary
Reads alignment
| Number of mapped reads (left/right): | 45,024,402 / 44,986,366 |
| Number of aligned pairs (without duplicates): | 44,957,766 |
| Total number of alignments: | 101,623,516 |
| Number of secondary alignments: | 11,612,748 |
| Number of non-unique alignments: | 13,014,608 |
| Aligned to genes: | 72,713,122 |
| Ambiguous alignments: | 270,558 |
| No feature assigned: | 11,845,704 |
| Missing chromosome in annotation: | 3,779,524 |
| Not aligned: | 2,173,854 |
Reads genomic origin
| Exonic: | 72,713,122 / 85.99% |
| Intronic: | 8,729,747 / 10.32% |
| Intergenic: | 3,115,957 / 3.68% |
| Intronic/intergenic overlapping exon: | 3,556,107 / 4.21% |
Transcript coverage profile
| 5' bias: | 0.47 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.91 |
Junction analysis
| Reads at junctions: | 28,119,339 |
| ACCT | 5.23% |
| AGGT | 4.75% |
| AGGA | 3.57% |
| TCCT | 3.55% |
| ATCT | 3.53% |
| GCCT | 2.85% |
| AGCT | 2.78% |
| CCCT | 2.47% |
| AGGC | 2.41% |
| AGAT | 2.3% |
| TTCT | 2.24% |
.png)
.png)
.png)
