Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:04:54 GMT 2023 |
| BAM file: | SRX7354358.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): | 42,797,565 / 42,711,422 |
| Number of aligned pairs (without duplicates): | 42,699,579 |
| Total number of alignments: | 93,329,116 |
| Number of secondary alignments: | 7,820,129 |
| Number of non-unique alignments: | 12,071,635 |
| Aligned to genes: | 72,395,820 |
| Ambiguous alignments: | 303,699 |
| No feature assigned: | 7,702,557 |
| Missing chromosome in annotation: | 855,405 |
| Not aligned: | 7,670,411 |
Reads genomic origin
| Exonic: | 72,395,820 / 90.38% |
| Intronic: | 5,017,387 / 6.26% |
| Intergenic: | 2,685,170 / 3.35% |
| Intronic/intergenic overlapping exon: | 3,132,959 / 3.91% |
Transcript coverage profile
| 5' bias: | 0.23 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.87 |
Junction analysis
| Reads at junctions: | 23,233,004 |
| ACCT | 5.4% |
| AGGT | 4.49% |
| TCCT | 4.18% |
| ATCT | 4.03% |
| AGGA | 3.15% |
| GCCT | 3.05% |
| CCCT | 2.67% |
| TTCT | 2.43% |
| AGCT | 2.23% |
| AGGC | 2.21% |
| AGAT | 1.79% |
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