Input data and parameters
Input
| Analysis date: | Sun Oct 29 02:27:51 GMT 2023 |
| BAM file: | SRX7354069.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): | 56,342,109 / 56,318,118 |
| Number of aligned pairs (without duplicates): | 56,311,546 |
| Total number of alignments: | 120,771,362 |
| Number of secondary alignments: | 8,111,135 |
| Number of non-unique alignments: | 13,442,984 |
| Aligned to genes: | 94,332,928 |
| Ambiguous alignments: | 339,189 |
| No feature assigned: | 12,013,333 |
| Missing chromosome in annotation: | 642,928 |
| Not aligned: | 2,962,341 |
Reads genomic origin
| Exonic: | 94,332,928 / 88.7% |
| Intronic: | 8,642,927 / 8.13% |
| Intergenic: | 3,370,406 / 3.17% |
| Intronic/intergenic overlapping exon: | 4,103,193 / 3.86% |
Transcript coverage profile
| 5' bias: | 0.25 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 1.91 |
Junction analysis
| Reads at junctions: | 31,293,488 |
| ACCT | 5.4% |
| AGGT | 4.67% |
| ATCT | 3.66% |
| TCCT | 3.49% |
| AGGA | 3.44% |
| GCCT | 3.19% |
| AGCT | 2.62% |
| TTCT | 2.45% |
| AGGC | 2.4% |
| CCCT | 2.37% |
| AGAT | 2.15% |

.png)
.png)
.png)

