Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:52:00 GMT 2023 |
| BAM file: | SRX7354330.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): | 44,876,832 / 44,805,443 |
| Number of aligned pairs (without duplicates): | 44,797,715 |
| Total number of alignments: | 95,887,429 |
| Number of secondary alignments: | 6,205,154 |
| Number of non-unique alignments: | 9,616,604 |
| Aligned to genes: | 73,211,538 |
| Ambiguous alignments: | 261,017 |
| No feature assigned: | 12,007,032 |
| Missing chromosome in annotation: | 791,238 |
| Not aligned: | 14,309,273 |
Reads genomic origin
| Exonic: | 73,211,538 / 85.91% |
| Intronic: | 7,214,591 / 8.47% |
| Intergenic: | 4,792,441 / 5.62% |
| Intronic/intergenic overlapping exon: | 3,276,302 / 3.84% |
Transcript coverage profile
| 5' bias: | 0.43 |
| 3' bias: | 0.29 |
| 5'-3' bias: | 1.74 |
Junction analysis
| Reads at junctions: | 26,028,734 |
| ACCT | 5.18% |
| AGGT | 4.77% |
| TCCT | 3.66% |
| ATCT | 3.65% |
| AGGA | 3.47% |
| GCCT | 3.01% |
| AGCT | 2.75% |
| CCCT | 2.63% |
| AGGC | 2.43% |
| TTCT | 2.14% |
| AGAT | 2.13% |

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