Input data and parameters
Input
| Analysis date: | Tue Oct 31 00:18:40 GMT 2023 |
| BAM file: | SRX7354291.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): | 29,969,050 / 29,956,669 |
| Number of aligned pairs (without duplicates): | 29,952,683 |
| Total number of alignments: | 67,712,871 |
| Number of secondary alignments: | 7,787,152 |
| Number of non-unique alignments: | 10,685,637 |
| Aligned to genes: | 42,211,088 |
| Ambiguous alignments: | 186,362 |
| No feature assigned: | 12,967,889 |
| Missing chromosome in annotation: | 1,661,895 |
| Not aligned: | 727,703 |
Reads genomic origin
| Exonic: | 42,211,088 / 76.5% |
| Intronic: | 5,976,040 / 10.83% |
| Intergenic: | 6,991,849 / 12.67% |
| Intronic/intergenic overlapping exon: | 2,172,805 / 3.94% |
Transcript coverage profile
| 5' bias: | 0.2 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 2.12 |
Junction analysis
| Reads at junctions: | 17,572,994 |
| TCCT | 5.42% |
| ACCT | 5.26% |
| ATCT | 4.47% |
| AGGT | 3.97% |
| CCCT | 3.22% |
| GCCT | 2.96% |
| AGGA | 2.63% |
| TCCC | 2.56% |
| GTCT | 2.48% |
| TTCT | 2.42% |
| AGGC | 2.1% |
.png)
.png)
.png)
