Input data and parameters
Input
| Analysis date: | Tue Oct 31 16:15:17 GMT 2023 |
| BAM file: | SRX7354389.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): | 51,309,619 / 51,280,118 |
| Number of aligned pairs (without duplicates): | 51,246,964 |
| Total number of alignments: | 109,799,601 |
| Number of secondary alignments: | 7,209,864 |
| Number of non-unique alignments: | 12,063,631 |
| Aligned to genes: | 86,784,590 |
| Ambiguous alignments: | 424,955 |
| No feature assigned: | 10,142,573 |
| Missing chromosome in annotation: | 383,852 |
| Not aligned: | 1,963,701 |
Reads genomic origin
| Exonic: | 86,784,590 / 89.54% |
| Intronic: | 6,592,713 / 6.8% |
| Intergenic: | 3,549,860 / 3.66% |
| Intronic/intergenic overlapping exon: | 4,623,846 / 4.77% |
Transcript coverage profile
| 5' bias: | 0.23 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.73 |
Junction analysis
| Reads at junctions: | 33,614,555 |
| ACCT | 5.18% |
| TCCT | 4.84% |
| ATCT | 4.76% |
| AGGT | 4.21% |
| CCCT | 3.36% |
| GCCT | 3.19% |
| AGGA | 2.91% |
| TTCT | 2.36% |
| AGGC | 2.3% |
| AGCT | 2.16% |
| GTCT | 1.99% |
.png)
.png)
.png)
