Input data and parameters
Input
| Analysis date: | Mon Oct 30 11:08:00 GMT 2023 |
| BAM file: | SRX7354169.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): | 35,480,002 / 35,455,077 |
| Number of aligned pairs (without duplicates): | 35,451,305 |
| Total number of alignments: | 75,229,006 |
| Number of secondary alignments: | 4,293,927 |
| Number of non-unique alignments: | 7,234,305 |
| Aligned to genes: | 58,191,198 |
| Ambiguous alignments: | 190,978 |
| No feature assigned: | 9,319,653 |
| Missing chromosome in annotation: | 292,872 |
| Not aligned: | 7,300,127 |
Reads genomic origin
| Exonic: | 58,191,198 / 86.2% |
| Intronic: | 5,833,759 / 8.64% |
| Intergenic: | 3,485,894 / 5.16% |
| Intronic/intergenic overlapping exon: | 2,390,007 / 3.54% |
Transcript coverage profile
| 5' bias: | 0.26 |
| 3' bias: | 0.14 |
| 5'-3' bias: | 2.33 |
Junction analysis
| Reads at junctions: | 16,390,684 |
| ACCT | 5.48% |
| AGGT | 4.73% |
| ATCT | 3.65% |
| AGGA | 3.59% |
| TCCT | 3.42% |
| GCCT | 3.09% |
| AGCT | 2.75% |
| AGGC | 2.38% |
| AGAT | 2.34% |
| CCCT | 2.31% |
| TTCT | 2.22% |
.png)
.png)
.png)
