Input data and parameters
Input
| Analysis date: | Sun Oct 29 02:05:52 GMT 2023 |
| BAM file: | SRX7354124.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): | 43,818,274 / 43,756,651 |
| Number of aligned pairs (without duplicates): | 43,741,720 |
| Total number of alignments: | 92,685,714 |
| Number of secondary alignments: | 5,110,789 |
| Number of non-unique alignments: | 8,643,914 |
| Aligned to genes: | 71,345,121 |
| Ambiguous alignments: | 204,702 |
| No feature assigned: | 12,174,338 |
| Missing chromosome in annotation: | 317,639 |
| Not aligned: | 7,222,245 |
Reads genomic origin
| Exonic: | 71,345,121 / 85.42% |
| Intronic: | 8,445,716 / 10.11% |
| Intergenic: | 3,728,622 / 4.46% |
| Intronic/intergenic overlapping exon: | 3,524,589 / 4.22% |
Transcript coverage profile
| 5' bias: | 0.31 |
| 3' bias: | 0.14 |
| 5'-3' bias: | 2.15 |
Junction analysis
| Reads at junctions: | 22,817,979 |
| ACCT | 5.36% |
| AGGT | 4.68% |
| AGGA | 3.69% |
| ATCT | 3.63% |
| TCCT | 3.38% |
| GCCT | 2.93% |
| AGCT | 2.71% |
| AGAT | 2.4% |
| AGGC | 2.33% |
| CCCT | 2.23% |
| TTCT | 2.2% |
.png)
.png)
.png)
