Input data and parameters
Input
| Analysis date: | Sun Oct 29 02:01:34 GMT 2023 |
| BAM file: | SRX7354126.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): | 51,731,630 / 51,676,716 |
| Number of aligned pairs (without duplicates): | 51,656,280 |
| Total number of alignments: | 114,520,880 |
| Number of secondary alignments: | 11,112,534 |
| Number of non-unique alignments: | 14,284,182 |
| Aligned to genes: | 85,322,404 |
| Ambiguous alignments: | 262,254 |
| No feature assigned: | 11,895,006 |
| Missing chromosome in annotation: | 2,757,034 |
| Not aligned: | 2,441,810 |
Reads genomic origin
| Exonic: | 85,322,404 / 87.76% |
| Intronic: | 8,234,434 / 8.47% |
| Intergenic: | 3,660,572 / 3.77% |
| Intronic/intergenic overlapping exon: | 3,855,580 / 3.97% |
Transcript coverage profile
| 5' bias: | 0.47 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.73 |
Junction analysis
| Reads at junctions: | 28,099,849 |
| ACCT | 4.88% |
| AGGT | 4.83% |
| ATCT | 3.66% |
| AGGA | 3.59% |
| TCCT | 3.58% |
| GCCT | 3.09% |
| AGCT | 3.01% |
| CCCT | 2.59% |
| AGGC | 2.41% |
| TTCT | 2.14% |
| AGAT | 2.1% |
.png)
.png)
.png)
