Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:29:46 GMT 2023 |
| BAM file: | SRX7354196.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): | 54,271,593 / 54,200,545 |
| Number of aligned pairs (without duplicates): | 54,183,176 |
| Total number of alignments: | 115,220,285 |
| Number of secondary alignments: | 6,748,147 |
| Number of non-unique alignments: | 11,548,081 |
| Aligned to genes: | 87,743,121 |
| Ambiguous alignments: | 265,878 |
| No feature assigned: | 15,315,608 |
| Missing chromosome in annotation: | 347,597 |
| Not aligned: | 8,087,236 |
Reads genomic origin
| Exonic: | 87,743,121 / 85.14% |
| Intronic: | 10,289,725 / 9.98% |
| Intergenic: | 5,025,883 / 4.88% |
| Intronic/intergenic overlapping exon: | 4,251,535 / 4.13% |
Transcript coverage profile
| 5' bias: | 0.3 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.03 |
Junction analysis
| Reads at junctions: | 25,064,274 |
| ACCT | 5.31% |
| AGGT | 4.81% |
| AGGA | 3.67% |
| ATCT | 3.63% |
| TCCT | 3.34% |
| GCCT | 2.94% |
| AGCT | 2.83% |
| CCCT | 2.43% |
| AGGC | 2.43% |
| AGAT | 2.41% |
| TTCT | 2.17% |
.png)
.png)
.png)
