Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:38:48 GMT 2023 |
| BAM file: | SRX7354398.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): | 42,957,175 / 42,665,456 |
| Number of aligned pairs (without duplicates): | 42,627,352 |
| Total number of alignments: | 94,883,475 |
| Number of secondary alignments: | 9,260,844 |
| Number of non-unique alignments: | 12,484,715 |
| Aligned to genes: | 61,500,583 |
| Ambiguous alignments: | 217,933 |
| No feature assigned: | 18,595,463 |
| Missing chromosome in annotation: | 2,084,781 |
| Not aligned: | 21,937,621 |
Reads genomic origin
| Exonic: | 61,500,583 / 76.78% |
| Intronic: | 8,650,594 / 10.8% |
| Intergenic: | 9,944,869 / 12.42% |
| Intronic/intergenic overlapping exon: | 3,573,068 / 4.46% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.24 |
| 5'-3' bias: | 1.86 |
Junction analysis
| Reads at junctions: | 20,779,013 |
| ACCT | 5.17% |
| AGGT | 4.7% |
| TCCT | 3.79% |
| ATCT | 3.74% |
| GCCT | 3.42% |
| AGGA | 3.27% |
| CCCT | 2.63% |
| AGCT | 2.61% |
| TTCT | 2.33% |
| AGGC | 2.31% |
| AGAT | 1.95% |
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