Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:46:56 GMT 2023 |
| BAM file: | SRX7354350.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): | 36,264,754 / 36,238,511 |
| Number of aligned pairs (without duplicates): | 36,233,555 |
| Total number of alignments: | 77,738,377 |
| Number of secondary alignments: | 5,235,112 |
| Number of non-unique alignments: | 8,432,839 |
| Aligned to genes: | 59,945,597 |
| Ambiguous alignments: | 202,316 |
| No feature assigned: | 8,637,649 |
| Missing chromosome in annotation: | 519,976 |
| Not aligned: | 3,286,887 |
Reads genomic origin
| Exonic: | 59,945,597 / 87.41% |
| Intronic: | 6,045,105 / 8.81% |
| Intergenic: | 2,592,544 / 3.78% |
| Intronic/intergenic overlapping exon: | 2,185,336 / 3.19% |
Transcript coverage profile
| 5' bias: | 0.43 |
| 3' bias: | 0.24 |
| 5'-3' bias: | 1.86 |
Junction analysis
| Reads at junctions: | 18,095,049 |
| ACCT | 5.31% |
| AGGT | 4.65% |
| ATCT | 3.6% |
| AGGA | 3.46% |
| GCCT | 3.42% |
| TCCT | 3.38% |
| AGCT | 2.72% |
| CCCT | 2.52% |
| AGGC | 2.36% |
| TTCT | 2.32% |
| AGAT | 2.21% |
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