Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:20:47 GMT 2023 |
| BAM file: | SRX7354146.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): | 41,826,372 / 41,785,163 |
| Number of aligned pairs (without duplicates): | 41,758,058 |
| Total number of alignments: | 89,989,708 |
| Number of secondary alignments: | 6,378,173 |
| Number of non-unique alignments: | 10,190,399 |
| Aligned to genes: | 68,429,947 |
| Ambiguous alignments: | 312,558 |
| No feature assigned: | 10,549,570 |
| Missing chromosome in annotation: | 507,234 |
| Not aligned: | 1,498,271 |
Reads genomic origin
| Exonic: | 68,429,947 / 86.64% |
| Intronic: | 8,381,224 / 10.61% |
| Intergenic: | 2,168,346 / 2.75% |
| Intronic/intergenic overlapping exon: | 3,736,947 / 4.73% |
Transcript coverage profile
| 5' bias: | 0.42 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 1.84 |
Junction analysis
| Reads at junctions: | 29,140,470 |
| ACCT | 5.28% |
| AGGT | 4.68% |
| TCCT | 3.64% |
| AGGA | 3.49% |
| ATCT | 3.37% |
| GCCT | 3% |
| AGCT | 2.74% |
| CCCT | 2.57% |
| AGGC | 2.52% |
| AGGG | 2.04% |
| AGAT | 2.04% |
.png)
.png)
.png)
