Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:22:36 GMT 2023 |
| BAM file: | SRX7354071.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): | 43,894,751 / 43,874,614 |
| Number of aligned pairs (without duplicates): | 43,867,255 |
| Total number of alignments: | 96,740,860 |
| Number of secondary alignments: | 8,971,495 |
| Number of non-unique alignments: | 13,305,514 |
| Aligned to genes: | 74,123,370 |
| Ambiguous alignments: | 322,227 |
| No feature assigned: | 7,631,213 |
| Missing chromosome in annotation: | 1,358,536 |
| Not aligned: | 2,457,257 |
Reads genomic origin
| Exonic: | 74,123,370 / 90.67% |
| Intronic: | 4,404,924 / 5.39% |
| Intergenic: | 3,226,289 / 3.95% |
| Intronic/intergenic overlapping exon: | 3,787,784 / 4.63% |
Transcript coverage profile
| 5' bias: | 0.11 |
| 3' bias: | 0.13 |
| 5'-3' bias: | 2.24 |
Junction analysis
| Reads at junctions: | 26,142,734 |
| TCCT | 5.54% |
| ACCT | 5.18% |
| ATCT | 4.42% |
| AGGT | 4.2% |
| CCCT | 3.37% |
| AGGA | 3.01% |
| GCCT | 2.36% |
| AGGC | 2.25% |
| TTCT | 2.18% |
| TCCC | 1.96% |
| AGCT | 1.91% |

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