Input data and parameters
Input
| Analysis date: | Tue Oct 31 17:17:40 GMT 2023 |
| BAM file: | SRX7354401.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): | 35,161,702 / 35,125,875 |
| Number of aligned pairs (without duplicates): | 35,122,511 |
| Total number of alignments: | 74,719,937 |
| Number of secondary alignments: | 4,432,360 |
| Number of non-unique alignments: | 7,374,221 |
| Aligned to genes: | 59,352,161 |
| Ambiguous alignments: | 221,891 |
| No feature assigned: | 7,467,863 |
| Missing chromosome in annotation: | 303,801 |
| Not aligned: | 6,827,319 |
Reads genomic origin
| Exonic: | 59,352,161 / 88.82% |
| Intronic: | 4,979,920 / 7.45% |
| Intergenic: | 2,487,943 / 3.72% |
| Intronic/intergenic overlapping exon: | 2,107,115 / 3.15% |
Transcript coverage profile
| 5' bias: | 0.36 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.93 |
Junction analysis
| Reads at junctions: | 19,942,023 |
| ACCT | 5.25% |
| AGGT | 4.76% |
| ATCT | 3.66% |
| AGGA | 3.54% |
| TCCT | 3.43% |
| GCCT | 3.11% |
| AGCT | 2.74% |
| TTCT | 2.37% |
| AGGC | 2.36% |
| CCCT | 2.36% |
| AGAT | 2.23% |
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