Input data and parameters
Input
| Analysis date: | Tue Oct 31 18:08:09 GMT 2023 |
| BAM file: | SRX7354403.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): | 53,575,022 / 53,530,134 |
| Number of aligned pairs (without duplicates): | 53,521,751 |
| Total number of alignments: | 113,705,171 |
| Number of secondary alignments: | 6,600,015 |
| Number of non-unique alignments: | 11,095,750 |
| Aligned to genes: | 88,668,174 |
| Ambiguous alignments: | 284,189 |
| No feature assigned: | 13,266,174 |
| Missing chromosome in annotation: | 390,884 |
| Not aligned: | 9,399,940 |
Reads genomic origin
| Exonic: | 88,668,174 / 86.99% |
| Intronic: | 8,399,372 / 8.24% |
| Intergenic: | 4,866,802 / 4.77% |
| Intronic/intergenic overlapping exon: | 3,678,841 / 3.61% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.96 |
Junction analysis
| Reads at junctions: | 28,778,570 |
| ACCT | 5.38% |
| AGGT | 4.64% |
| ATCT | 3.75% |
| TCCT | 3.6% |
| AGGA | 3.47% |
| GCCT | 3.25% |
| AGCT | 2.66% |
| AGGC | 2.46% |
| CCCT | 2.41% |
| AGAT | 2.25% |
| TTCT | 2.23% |

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