Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:02:25 GMT 2023 |
| BAM file: | SRX7354379.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): | 45,605,018 / 45,578,202 |
| Number of aligned pairs (without duplicates): | 45,557,191 |
| Total number of alignments: | 98,959,164 |
| Number of secondary alignments: | 7,775,944 |
| Number of non-unique alignments: | 12,968,935 |
| Aligned to genes: | 75,062,036 |
| Ambiguous alignments: | 307,213 |
| No feature assigned: | 10,022,293 |
| Missing chromosome in annotation: | 598,687 |
| Not aligned: | 2,084,512 |
Reads genomic origin
| Exonic: | 75,062,036 / 88.22% |
| Intronic: | 6,511,748 / 7.65% |
| Intergenic: | 3,510,545 / 4.13% |
| Intronic/intergenic overlapping exon: | 3,710,751 / 4.36% |
Transcript coverage profile
| 5' bias: | 0.42 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 1.89 |
Junction analysis
| Reads at junctions: | 27,115,102 |
| ACCT | 5.34% |
| AGGT | 4.51% |
| TCCT | 3.95% |
| ATCT | 3.88% |
| GCCT | 3.53% |
| AGGA | 3.19% |
| CCCT | 2.92% |
| AGCT | 2.56% |
| AGGC | 2.38% |
| TTCT | 2.12% |
| AGAT | 1.84% |

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