Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:58:09 GMT 2023 |
| BAM file: | SRX7354345.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): | 48,340,633 / 48,272,027 |
| Number of aligned pairs (without duplicates): | 48,264,211 |
| Total number of alignments: | 103,230,966 |
| Number of secondary alignments: | 6,618,306 |
| Number of non-unique alignments: | 10,552,453 |
| Aligned to genes: | 75,749,067 |
| Ambiguous alignments: | 308,048 |
| No feature assigned: | 16,181,452 |
| Missing chromosome in annotation: | 439,946 |
| Not aligned: | 8,794,340 |
Reads genomic origin
| Exonic: | 75,749,067 / 82.4% |
| Intronic: | 12,716,535 / 13.83% |
| Intergenic: | 3,464,917 / 3.77% |
| Intronic/intergenic overlapping exon: | 3,208,859 / 3.49% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 1.92 |
Junction analysis
| Reads at junctions: | 26,687,230 |
| ACCT | 5.53% |
| AGGT | 4.75% |
| AGGA | 3.66% |
| ATCT | 3.5% |
| TCCT | 3.47% |
| AGCT | 2.69% |
| GCCT | 2.64% |
| TTCT | 2.45% |
| AGAT | 2.45% |
| AGGC | 2.33% |
| CCCT | 2.31% |
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