Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:29:52 GMT 2023 |
| BAM file: | SRX7354327.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): | 38,589,868 / 38,541,275 |
| Number of aligned pairs (without duplicates): | 38,534,944 |
| Total number of alignments: | 82,976,778 |
| Number of secondary alignments: | 5,845,635 |
| Number of non-unique alignments: | 9,607,361 |
| Aligned to genes: | 64,189,427 |
| Ambiguous alignments: | 230,023 |
| No feature assigned: | 8,452,255 |
| Missing chromosome in annotation: | 497,712 |
| Not aligned: | 10,529,167 |
Reads genomic origin
| Exonic: | 64,189,427 / 88.36% |
| Intronic: | 5,303,880 / 7.3% |
| Intergenic: | 3,148,375 / 4.33% |
| Intronic/intergenic overlapping exon: | 2,416,819 / 3.33% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 2 |
Junction analysis
| Reads at junctions: | 19,813,294 |
| ACCT | 5.55% |
| AGGT | 4.86% |
| ATCT | 3.6% |
| TCCT | 3.53% |
| AGGA | 3.52% |
| GCCT | 3.13% |
| CCCT | 2.57% |
| AGCT | 2.55% |
| AGGC | 2.41% |
| AGAT | 2.17% |
| TTCT | 2.1% |
.png)
.png)
.png)
