Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:31:54 GMT 2023 |
| BAM file: | SRX7354360.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): | 57,893,283 / 57,820,585 |
| Number of aligned pairs (without duplicates): | 57,805,463 |
| Total number of alignments: | 124,582,113 |
| Number of secondary alignments: | 8,868,245 |
| Number of non-unique alignments: | 14,727,861 |
| Aligned to genes: | 98,164,991 |
| Ambiguous alignments: | 410,652 |
| No feature assigned: | 10,618,281 |
| Missing chromosome in annotation: | 660,328 |
| Not aligned: | 6,784,698 |
Reads genomic origin
| Exonic: | 98,164,991 / 90.24% |
| Intronic: | 6,190,393 / 5.69% |
| Intergenic: | 4,427,888 / 4.07% |
| Intronic/intergenic overlapping exon: | 4,275,585 / 3.93% |
Transcript coverage profile
| 5' bias: | 0.23 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2 |
Junction analysis
| Reads at junctions: | 30,641,264 |
| ACCT | 5.32% |
| ATCT | 4.61% |
| AGGT | 4.4% |
| TCCT | 4.3% |
| GCCT | 3.31% |
| AGGA | 3.12% |
| CCCT | 2.93% |
| AGCT | 2.26% |
| TTCT | 2.18% |
| AGGC | 2.15% |
| AGAA | 1.79% |
.png)
.png)
.png)
