Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:23:17 GMT 2023 |
| BAM file: | SRX7354220.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): | 42,567,660 / 42,543,232 |
| Number of aligned pairs (without duplicates): | 42,539,468 |
| Total number of alignments: | 90,586,765 |
| Number of secondary alignments: | 5,475,873 |
| Number of non-unique alignments: | 9,205,517 |
| Aligned to genes: | 72,381,119 |
| Ambiguous alignments: | 274,588 |
| No feature assigned: | 8,395,995 |
| Missing chromosome in annotation: | 329,546 |
| Not aligned: | 3,313,272 |
Reads genomic origin
| Exonic: | 72,381,119 / 89.61% |
| Intronic: | 5,539,913 / 6.86% |
| Intergenic: | 2,856,082 / 3.54% |
| Intronic/intergenic overlapping exon: | 2,523,726 / 3.12% |
Transcript coverage profile
| 5' bias: | 0.35 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.9 |
Junction analysis
| Reads at junctions: | 24,057,603 |
| ACCT | 5.28% |
| AGGT | 4.62% |
| ATCT | 3.62% |
| AGGA | 3.51% |
| TCCT | 3.49% |
| GCCT | 3.12% |
| AGCT | 2.75% |
| AGGC | 2.44% |
| CCCT | 2.42% |
| AGAT | 2.23% |
| TTCT | 2.23% |
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