Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:37:10 GMT 2023 |
| BAM file: | SRX7354251.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): | 38,353,926 / 38,335,712 |
| Number of aligned pairs (without duplicates): | 38,332,917 |
| Total number of alignments: | 80,800,224 |
| Number of secondary alignments: | 4,110,586 |
| Number of non-unique alignments: | 6,935,810 |
| Aligned to genes: | 64,523,474 |
| Ambiguous alignments: | 203,920 |
| No feature assigned: | 8,884,055 |
| Missing chromosome in annotation: | 252,965 |
| Not aligned: | 2,799,086 |
Reads genomic origin
| Exonic: | 64,523,474 / 87.9% |
| Intronic: | 5,850,814 / 7.97% |
| Intergenic: | 3,033,241 / 4.13% |
| Intronic/intergenic overlapping exon: | 2,657,188 / 3.62% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.15 |
Junction analysis
| Reads at junctions: | 20,519,120 |
| ACCT | 5.41% |
| AGGT | 4.81% |
| ATCT | 3.71% |
| AGGA | 3.59% |
| TCCT | 3.4% |
| GCCT | 3.03% |
| AGCT | 2.73% |
| CCCT | 2.46% |
| AGGC | 2.41% |
| AGAT | 2.3% |
| TTCT | 2.07% |
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