Input data and parameters
Input
| Analysis date: | Tue Oct 31 17:45:45 GMT 2023 |
| BAM file: | SRX7354409.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): | 56,903,112 / 56,866,497 |
| Number of aligned pairs (without duplicates): | 56,861,803 |
| Total number of alignments: | 122,002,576 |
| Number of secondary alignments: | 8,232,967 |
| Number of non-unique alignments: | 12,661,324 |
| Aligned to genes: | 88,121,710 |
| Ambiguous alignments: | 345,631 |
| No feature assigned: | 19,886,966 |
| Missing chromosome in annotation: | 986,945 |
| Not aligned: | 4,511,863 |
Reads genomic origin
| Exonic: | 88,121,710 / 81.59% |
| Intronic: | 13,946,910 / 12.91% |
| Intergenic: | 5,940,056 / 5.5% |
| Intronic/intergenic overlapping exon: | 3,942,835 / 3.65% |
Transcript coverage profile
| 5' bias: | 0.53 |
| 3' bias: | 0.33 |
| 5'-3' bias: | 1.65 |
Junction analysis
| Reads at junctions: | 36,835,913 |
| ACCT | 5.21% |
| AGGT | 4.66% |
| TCCT | 3.53% |
| AGGA | 3.41% |
| GCCT | 3.36% |
| ATCT | 3.35% |
| AGCT | 2.8% |
| CCCT | 2.59% |
| AGGC | 2.46% |
| AGAT | 2.18% |
| TTCT | 2.09% |

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