Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:35:24 GMT 2023 |
| BAM file: | SRX7354237.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): | 47,669,839 / 47,627,367 |
| Number of aligned pairs (without duplicates): | 47,612,868 |
| Total number of alignments: | 102,191,557 |
| Number of secondary alignments: | 6,894,351 |
| Number of non-unique alignments: | 10,774,188 |
| Aligned to genes: | 80,864,859 |
| Ambiguous alignments: | 262,963 |
| No feature assigned: | 9,612,743 |
| Missing chromosome in annotation: | 676,804 |
| Not aligned: | 5,377,254 |
Reads genomic origin
| Exonic: | 80,864,859 / 89.38% |
| Intronic: | 6,952,575 / 7.68% |
| Intergenic: | 2,660,168 / 2.94% |
| Intronic/intergenic overlapping exon: | 3,898,836 / 4.31% |
Transcript coverage profile
| 5' bias: | 0.32 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.75 |
Junction analysis
| Reads at junctions: | 28,975,106 |
| AGGT | 4.86% |
| ACCT | 4.84% |
| ATCT | 4.76% |
| TCCT | 4.28% |
| AGGA | 3.45% |
| AGCT | 2.82% |
| GCCT | 2.64% |
| AGGC | 2.35% |
| CCCT | 2.29% |
| AGAT | 1.94% |
| TTCT | 1.83% |
.png)
.png)
.png)
