Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:51:51 GMT 2023 |
| BAM file: | SRX7354161.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): | 34,191,465 / 34,171,478 |
| Number of aligned pairs (without duplicates): | 34,167,863 |
| Total number of alignments: | 72,666,331 |
| Number of secondary alignments: | 4,303,388 |
| Number of non-unique alignments: | 6,893,391 |
| Aligned to genes: | 58,001,234 |
| Ambiguous alignments: | 209,823 |
| No feature assigned: | 7,149,163 |
| Missing chromosome in annotation: | 412,720 |
| Not aligned: | 1,784,577 |
Reads genomic origin
| Exonic: | 58,001,234 / 89.03% |
| Intronic: | 5,085,272 / 7.81% |
| Intergenic: | 2,063,891 / 3.17% |
| Intronic/intergenic overlapping exon: | 2,083,076 / 3.2% |
Transcript coverage profile
| 5' bias: | 0.35 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.75 |
Junction analysis
| Reads at junctions: | 19,090,308 |
| ACCT | 5.32% |
| AGGT | 4.56% |
| ATCT | 3.61% |
| TCCT | 3.55% |
| AGGA | 3.37% |
| GCCT | 3.36% |
| AGCT | 2.68% |
| CCCT | 2.44% |
| TTCT | 2.34% |
| AGGC | 2.32% |
| AGAT | 2.09% |
.png)
.png)
.png)
