Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:25:44 GMT 2023 |
| BAM file: | SRX7354263.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): | 31,739,100 / 31,702,146 |
| Number of aligned pairs (without duplicates): | 31,691,248 |
| Total number of alignments: | 67,886,239 |
| Number of secondary alignments: | 4,444,993 |
| Number of non-unique alignments: | 7,157,317 |
| Aligned to genes: | 54,084,209 |
| Ambiguous alignments: | 182,103 |
| No feature assigned: | 6,010,572 |
| Missing chromosome in annotation: | 452,038 |
| Not aligned: | 5,614,372 |
Reads genomic origin
| Exonic: | 54,084,209 / 90% |
| Intronic: | 3,363,418 / 5.6% |
| Intergenic: | 2,647,154 / 4.4% |
| Intronic/intergenic overlapping exon: | 2,202,253 / 3.66% |
Transcript coverage profile
| 5' bias: | 0.33 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2.13 |
Junction analysis
| Reads at junctions: | 17,883,484 |
| ACCT | 5.44% |
| AGGT | 4.66% |
| ATCT | 3.62% |
| TCCT | 3.58% |
| AGGA | 3.43% |
| GCCT | 3.12% |
| AGCT | 2.69% |
| AGGC | 2.4% |
| CCCT | 2.36% |
| TTCT | 2.24% |
| AGAT | 2.18% |

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