Input data and parameters
Input
| Analysis date: | Mon Oct 30 09:53:57 GMT 2023 |
| BAM file: | SRX7354104.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): | 72,100,340 / 72,056,285 |
| Number of aligned pairs (without duplicates): | 72,045,443 |
| Total number of alignments: | 155,246,628 |
| Number of secondary alignments: | 11,090,003 |
| Number of non-unique alignments: | 17,401,762 |
| Aligned to genes: | 126,436,936 |
| Ambiguous alignments: | 504,321 |
| No feature assigned: | 9,825,470 |
| Missing chromosome in annotation: | 1,078,139 |
| Not aligned: | 5,082,159 |
Reads genomic origin
| Exonic: | 126,436,936 / 92.79% |
| Intronic: | 6,367,878 / 4.67% |
| Intergenic: | 3,457,592 / 2.54% |
| Intronic/intergenic overlapping exon: | 4,977,528 / 3.65% |
Transcript coverage profile
| 5' bias: | 0.19 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 2.1 |
Junction analysis
| Reads at junctions: | 53,325,136 |
| ACCT | 5.42% |
| TCCT | 4.9% |
| AGGT | 4.63% |
| ATCT | 4.35% |
| AGGA | 3.11% |
| CCCT | 2.73% |
| GCCT | 2.68% |
| AGGC | 2.19% |
| AGCT | 2.1% |
| TTCT | 2.02% |
| AGAA | 1.91% |
.png)
.png)
.png)
