Input data and parameters
Input
| Analysis date: | Mon Oct 30 09:43:07 GMT 2023 |
| BAM file: | SRX7354142.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): | 44,340,367 / 44,316,511 |
| Number of aligned pairs (without duplicates): | 44,310,807 |
| Total number of alignments: | 97,107,115 |
| Number of secondary alignments: | 8,450,237 |
| Number of non-unique alignments: | 13,339,540 |
| Aligned to genes: | 73,334,836 |
| Ambiguous alignments: | 244,639 |
| No feature assigned: | 9,169,008 |
| Missing chromosome in annotation: | 1,019,092 |
| Not aligned: | 2,417,198 |
Reads genomic origin
| Exonic: | 73,334,836 / 88.89% |
| Intronic: | 6,301,732 / 7.64% |
| Intergenic: | 2,867,276 / 3.48% |
| Intronic/intergenic overlapping exon: | 3,554,267 / 4.31% |
Transcript coverage profile
| 5' bias: | 0.32 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2 |
Junction analysis
| Reads at junctions: | 22,498,601 |
| ACCT | 5.26% |
| AGGT | 4.72% |
| ATCT | 3.65% |
| AGGA | 3.58% |
| TCCT | 3.5% |
| GCCT | 3.04% |
| AGCT | 2.66% |
| CCCT | 2.41% |
| AGGC | 2.33% |
| AGAT | 2.18% |
| TTCT | 2.15% |
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