Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:43:33 GMT 2023 |
| BAM file: | SRX7354079.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): | 50,951,465 / 50,874,826 |
| Number of aligned pairs (without duplicates): | 50,867,287 |
| Total number of alignments: | 110,182,154 |
| Number of secondary alignments: | 8,355,863 |
| Number of non-unique alignments: | 14,510,627 |
| Aligned to genes: | 83,973,803 |
| Ambiguous alignments: | 284,278 |
| No feature assigned: | 10,995,644 |
| Missing chromosome in annotation: | 417,802 |
| Not aligned: | 11,835,941 |
Reads genomic origin
| Exonic: | 83,973,803 / 88.42% |
| Intronic: | 6,604,481 / 6.95% |
| Intergenic: | 4,391,163 / 4.62% |
| Intronic/intergenic overlapping exon: | 3,995,089 / 4.21% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.24 |
| 5'-3' bias: | 1.78 |
Junction analysis
| Reads at junctions: | 27,214,838 |
| ACCT | 5.45% |
| AGGT | 4.49% |
| GCCT | 3.65% |
| ATCT | 3.64% |
| TCCT | 3.41% |
| AGGA | 3.31% |
| AGCT | 2.68% |
| TTCT | 2.51% |
| CCCT | 2.49% |
| AGGC | 2.35% |
| AGAT | 2.1% |
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