Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:06:53 GMT 2023 |
| BAM file: | SRX7354362.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): | 43,978,881 / 43,919,166 |
| Number of aligned pairs (without duplicates): | 43,886,241 |
| Total number of alignments: | 95,586,212 |
| Number of secondary alignments: | 7,688,165 |
| Number of non-unique alignments: | 12,424,656 |
| Aligned to genes: | 75,155,826 |
| Ambiguous alignments: | 322,107 |
| No feature assigned: | 7,228,997 |
| Missing chromosome in annotation: | 454,626 |
| Not aligned: | 8,659,603 |
Reads genomic origin
| Exonic: | 75,155,826 / 91.23% |
| Intronic: | 4,574,525 / 5.55% |
| Intergenic: | 2,654,472 / 3.22% |
| Intronic/intergenic overlapping exon: | 2,726,090 / 3.31% |
Transcript coverage profile
| 5' bias: | 0.11 |
| 3' bias: | 0.13 |
| 5'-3' bias: | 1.84 |
Junction analysis
| Reads at junctions: | 23,923,474 |
| ACCT | 5.76% |
| AGGT | 4.71% |
| TCCT | 4.27% |
| ATCT | 3.79% |
| AGGA | 3.33% |
| CCCT | 2.64% |
| GCCT | 2.4% |
| AGGC | 2.23% |
| AGCT | 2.02% |
| TTCT | 1.83% |
| AGAT | 1.79% |
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