Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:34:25 GMT 2023 |
| BAM file: | SRX7354377.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): | 30,554,420 / 30,538,403 |
| Number of aligned pairs (without duplicates): | 30,535,503 |
| Total number of alignments: | 64,933,637 |
| Number of secondary alignments: | 3,840,814 |
| Number of non-unique alignments: | 6,333,335 |
| Aligned to genes: | 50,371,200 |
| Ambiguous alignments: | 183,892 |
| No feature assigned: | 7,778,469 |
| Missing chromosome in annotation: | 266,741 |
| Not aligned: | 1,655,197 |
Reads genomic origin
| Exonic: | 50,371,200 / 86.62% |
| Intronic: | 5,613,385 / 9.65% |
| Intergenic: | 2,165,084 / 3.72% |
| Intronic/intergenic overlapping exon: | 1,936,644 / 3.33% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2.01 |
Junction analysis
| Reads at junctions: | 16,041,365 |
| ACCT | 5.33% |
| AGGT | 4.68% |
| ATCT | 3.58% |
| AGGA | 3.56% |
| TCCT | 3.4% |
| GCCT | 3.24% |
| AGCT | 2.75% |
| CCCT | 2.41% |
| AGGC | 2.37% |
| AGAT | 2.29% |
| TTCT | 2.17% |

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