Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:33:29 GMT 2023 |
| BAM file: | SRX7354296.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): | 39,150,823 / 39,128,565 |
| Number of aligned pairs (without duplicates): | 39,124,975 |
| Total number of alignments: | 83,265,369 |
| Number of secondary alignments: | 4,985,981 |
| Number of non-unique alignments: | 8,532,303 |
| Aligned to genes: | 66,420,878 |
| Ambiguous alignments: | 213,951 |
| No feature assigned: | 7,810,287 |
| Missing chromosome in annotation: | 287,950 |
| Not aligned: | 2,608,366 |
Reads genomic origin
| Exonic: | 66,420,878 / 89.48% |
| Intronic: | 4,887,428 / 6.58% |
| Intergenic: | 2,922,859 / 3.94% |
| Intronic/intergenic overlapping exon: | 2,426,467 / 3.27% |
Transcript coverage profile
| 5' bias: | 0.31 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 1.98 |
Junction analysis
| Reads at junctions: | 20,003,816 |
| ACCT | 5.35% |
| AGGT | 4.57% |
| ATCT | 3.68% |
| AGGA | 3.5% |
| TCCT | 3.32% |
| GCCT | 3.27% |
| AGCT | 2.74% |
| CCCT | 2.37% |
| AGGC | 2.33% |
| AGAT | 2.22% |
| TTCT | 2.18% |
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