Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:52:50 GMT 2023 |
| BAM file: | SRX7354372.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): | 27,369,383 / 27,351,515 |
| Number of aligned pairs (without duplicates): | 27,348,120 |
| Total number of alignments: | 58,297,497 |
| Number of secondary alignments: | 3,576,599 |
| Number of non-unique alignments: | 5,918,889 |
| Aligned to genes: | 46,010,813 |
| Ambiguous alignments: | 166,217 |
| No feature assigned: | 5,946,610 |
| Missing chromosome in annotation: | 254,968 |
| Not aligned: | 1,856,902 |
Reads genomic origin
| Exonic: | 46,010,813 / 88.55% |
| Intronic: | 3,901,775 / 7.51% |
| Intergenic: | 2,044,835 / 3.94% |
| Intronic/intergenic overlapping exon: | 1,704,629 / 3.28% |
Transcript coverage profile
| 5' bias: | 0.36 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 2.1 |
Junction analysis
| Reads at junctions: | 13,551,106 |
| ACCT | 5.23% |
| AGGT | 4.67% |
| ATCT | 3.73% |
| TCCT | 3.61% |
| AGGA | 3.54% |
| GCCT | 3.03% |
| AGCT | 2.62% |
| CCCT | 2.54% |
| AGGC | 2.34% |
| TTCT | 2.28% |
| AGAT | 2.2% |

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