Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:41:45 GMT 2023 |
| BAM file: | SRX7354070.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): | 39,418,647 / 39,398,841 |
| Number of aligned pairs (without duplicates): | 39,395,911 |
| Total number of alignments: | 84,010,913 |
| Number of secondary alignments: | 5,193,425 |
| Number of non-unique alignments: | 8,613,591 |
| Aligned to genes: | 66,857,187 |
| Ambiguous alignments: | 261,619 |
| No feature assigned: | 7,946,159 |
| Missing chromosome in annotation: | 332,357 |
| Not aligned: | 3,207,988 |
Reads genomic origin
| Exonic: | 66,857,187 / 89.38% |
| Intronic: | 5,374,878 / 7.19% |
| Intergenic: | 2,571,281 / 3.44% |
| Intronic/intergenic overlapping exon: | 2,255,456 / 3.02% |
Transcript coverage profile
| 5' bias: | 0.33 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.77 |
Junction analysis
| Reads at junctions: | 22,476,620 |
| ACCT | 5.43% |
| AGGT | 4.65% |
| ATCT | 3.63% |
| TCCT | 3.62% |
| AGGA | 3.41% |
| GCCT | 3.28% |
| AGCT | 2.7% |
| CCCT | 2.49% |
| AGGC | 2.36% |
| AGAT | 2.13% |
| TTCT | 2.1% |
.png)
.png)
.png)
