Input data and parameters
Input
| Analysis date: | Mon Oct 30 13:03:09 GMT 2023 |
| BAM file: | SRX7354208.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): | 56,228,801 / 56,155,407 |
| Number of aligned pairs (without duplicates): | 56,130,702 |
| Total number of alignments: | 120,547,792 |
| Number of secondary alignments: | 8,163,584 |
| Number of non-unique alignments: | 12,342,100 |
| Aligned to genes: | 92,451,525 |
| Ambiguous alignments: | 371,631 |
| No feature assigned: | 14,209,486 |
| Missing chromosome in annotation: | 1,173,050 |
| Not aligned: | 2,411,982 |
Reads genomic origin
| Exonic: | 92,451,525 / 86.68% |
| Intronic: | 10,235,938 / 9.6% |
| Intergenic: | 3,973,548 / 3.73% |
| Intronic/intergenic overlapping exon: | 4,896,593 / 4.59% |
Transcript coverage profile
| 5' bias: | 0.49 |
| 3' bias: | 0.24 |
| 5'-3' bias: | 1.73 |
Junction analysis
| Reads at junctions: | 35,158,914 |
| ACCT | 5.27% |
| AGGT | 4.7% |
| ATCT | 3.7% |
| TCCT | 3.42% |
| AGGA | 3.36% |
| GCCT | 3.33% |
| CCCT | 2.83% |
| AGCT | 2.7% |
| AGGC | 2.42% |
| TTCT | 2.16% |
| AGAT | 2.07% |
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