Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:32:41 GMT 2023 |
| BAM file: | SRX7354174.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): | 24,391,287 / 24,369,594 |
| Number of aligned pairs (without duplicates): | 24,367,368 |
| Total number of alignments: | 52,696,887 |
| Number of secondary alignments: | 3,936,006 |
| Number of non-unique alignments: | 5,659,039 |
| Aligned to genes: | 42,011,593 |
| Ambiguous alignments: | 183,673 |
| No feature assigned: | 4,177,882 |
| Missing chromosome in annotation: | 664,700 |
| Not aligned: | 2,150,599 |
Reads genomic origin
| Exonic: | 42,011,593 / 90.95% |
| Intronic: | 2,513,010 / 5.44% |
| Intergenic: | 1,664,872 / 3.6% |
| Intronic/intergenic overlapping exon: | 1,470,901 / 3.18% |
Transcript coverage profile
| 5' bias: | 0.26 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.87 |
Junction analysis
| Reads at junctions: | 13,987,444 |
| ACCT | 5.38% |
| AGGT | 4.7% |
| ATCT | 4.04% |
| TCCT | 3.91% |
| GCCT | 3.25% |
| AGGA | 3.2% |
| CCCT | 2.64% |
| AGCT | 2.37% |
| TTCT | 2.37% |
| AGGC | 2.24% |
| AGAA | 1.93% |
.png)
.png)
.png)
