Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:26:23 GMT 2023 |
| BAM file: | SRX7354074.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): | 91,252,929 / 91,043,857 |
| Number of aligned pairs (without duplicates): | 91,027,741 |
| Total number of alignments: | 195,027,732 |
| Number of secondary alignments: | 12,730,946 |
| Number of non-unique alignments: | 20,435,273 |
| Aligned to genes: | 145,789,904 |
| Ambiguous alignments: | 573,821 |
| No feature assigned: | 27,080,025 |
| Missing chromosome in annotation: | 1,148,709 |
| Not aligned: | 23,316,472 |
Reads genomic origin
| Exonic: | 145,789,904 / 84.34% |
| Intronic: | 16,343,125 / 9.45% |
| Intergenic: | 10,736,900 / 6.21% |
| Intronic/intergenic overlapping exon: | 6,816,246 / 3.94% |
Transcript coverage profile
| 5' bias: | 0.39 |
| 3' bias: | 0.32 |
| 5'-3' bias: | 1.62 |
Junction analysis
| Reads at junctions: | 57,521,364 |
| ACCT | 5.07% |
| AGGT | 4.7% |
| TCCT | 3.93% |
| ATCT | 3.73% |
| GCCT | 3.28% |
| AGGA | 3.16% |
| CCCT | 2.8% |
| AGCT | 2.56% |
| AGGC | 2.52% |
| TTCT | 2.19% |
| AGAT | 1.89% |

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