Input data and parameters
Input
| Analysis date: | Sun Oct 29 11:46:16 GMT 2023 |
| BAM file: | SRX7354075.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): | 46,237,060 / 46,207,369 |
| Number of aligned pairs (without duplicates): | 46,199,620 |
| Total number of alignments: | 101,510,585 |
| Number of secondary alignments: | 9,066,156 |
| Number of non-unique alignments: | 12,903,017 |
| Aligned to genes: | 79,998,365 |
| Ambiguous alignments: | 390,426 |
| No feature assigned: | 6,630,267 |
| Missing chromosome in annotation: | 1,588,510 |
| Not aligned: | 2,564,031 |
Reads genomic origin
| Exonic: | 79,998,365 / 92.35% |
| Intronic: | 3,902,471 / 4.5% |
| Intergenic: | 2,727,796 / 3.15% |
| Intronic/intergenic overlapping exon: | 3,592,599 / 4.15% |
Transcript coverage profile
| 5' bias: | 0.11 |
| 3' bias: | 0.12 |
| 5'-3' bias: | 2.14 |
Junction analysis
| Reads at junctions: | 26,631,656 |
| TCCT | 5.95% |
| ACCT | 5.33% |
| ATCT | 4.65% |
| AGGT | 4.16% |
| CCCT | 3.67% |
| AGGA | 2.87% |
| GCCT | 2.23% |
| AGGC | 2.21% |
| GTCT | 2.07% |
| TCCC | 1.97% |
| AGCT | 1.93% |
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