Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:10:02 GMT 2023 |
| BAM file: | SRX7354052.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): | 31,087,757 / 31,067,692 |
| Number of aligned pairs (without duplicates): | 31,064,530 |
| Total number of alignments: | 66,004,632 |
| Number of secondary alignments: | 3,849,183 |
| Number of non-unique alignments: | 6,351,084 |
| Aligned to genes: | 50,607,204 |
| Ambiguous alignments: | 187,167 |
| No feature assigned: | 8,598,057 |
| Missing chromosome in annotation: | 261,120 |
| Not aligned: | 2,653,343 |
Reads genomic origin
| Exonic: | 50,607,204 / 85.48% |
| Intronic: | 6,522,209 / 11.02% |
| Intergenic: | 2,075,848 / 3.51% |
| Intronic/intergenic overlapping exon: | 2,037,765 / 3.44% |
Transcript coverage profile
| 5' bias: | 0.35 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 2.28 |
Junction analysis
| Reads at junctions: | 17,036,006 |
| ACCT | 5.42% |
| AGGT | 4.69% |
| TCCT | 3.61% |
| AGGA | 3.59% |
| ATCT | 3.49% |
| GCCT | 2.97% |
| AGCT | 2.69% |
| AGGC | 2.38% |
| AGAT | 2.31% |
| CCCT | 2.3% |
| AGGG | 1.99% |
.png)
.png)
.png)
