Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:16:05 GMT 2023 |
| BAM file: | SRX7354369.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): | 33,611,551 / 33,586,772 |
| Number of aligned pairs (without duplicates): | 33,581,637 |
| Total number of alignments: | 72,896,790 |
| Number of secondary alignments: | 5,698,467 |
| Number of non-unique alignments: | 8,773,058 |
| Aligned to genes: | 53,968,390 |
| Ambiguous alignments: | 219,442 |
| No feature assigned: | 9,283,782 |
| Missing chromosome in annotation: | 652,118 |
| Not aligned: | 3,771,281 |
Reads genomic origin
| Exonic: | 53,968,390 / 85.32% |
| Intronic: | 7,108,273 / 11.24% |
| Intergenic: | 2,175,509 / 3.44% |
| Intronic/intergenic overlapping exon: | 1,840,045 / 2.91% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.89 |
Junction analysis
| Reads at junctions: | 19,284,399 |
| ACCT | 5.48% |
| AGGT | 4.5% |
| TCCT | 3.6% |
| ATCT | 3.52% |
| AGGA | 3.48% |
| GCCT | 3.29% |
| AGCT | 2.71% |
| CCCT | 2.42% |
| AGGC | 2.27% |
| AGAT | 2.25% |
| TTCT | 2.18% |
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