Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:48:09 GMT 2023 |
| BAM file: | SRX7354141.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): | 52,098,285 / 52,057,654 |
| Number of aligned pairs (without duplicates): | 52,052,614 |
| Total number of alignments: | 110,898,944 |
| Number of secondary alignments: | 6,743,005 |
| Number of non-unique alignments: | 11,284,100 |
| Aligned to genes: | 84,459,474 |
| Ambiguous alignments: | 316,399 |
| No feature assigned: | 14,418,226 |
| Missing chromosome in annotation: | 420,745 |
| Not aligned: | 3,401,383 |
Reads genomic origin
| Exonic: | 84,459,474 / 85.42% |
| Intronic: | 10,142,194 / 10.26% |
| Intergenic: | 4,276,032 / 4.32% |
| Intronic/intergenic overlapping exon: | 3,363,176 / 3.4% |
Transcript coverage profile
| 5' bias: | 0.39 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.83 |
Junction analysis
| Reads at junctions: | 27,875,792 |
| ACCT | 5.37% |
| AGGT | 4.7% |
| AGGA | 3.55% |
| ATCT | 3.48% |
| TCCT | 3.43% |
| GCCT | 3.18% |
| AGCT | 2.75% |
| CCCT | 2.45% |
| AGGC | 2.4% |
| AGAT | 2.32% |
| TTCT | 2.15% |

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