Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:52:31 GMT 2023 |
| BAM file: | SRX7354163.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): | 43,943,341 / 43,912,079 |
| Number of aligned pairs (without duplicates): | 43,908,556 |
| Total number of alignments: | 94,359,579 |
| Number of secondary alignments: | 6,504,159 |
| Number of non-unique alignments: | 10,156,518 |
| Aligned to genes: | 72,638,903 |
| Ambiguous alignments: | 235,389 |
| No feature assigned: | 10,570,707 |
| Missing chromosome in annotation: | 758,062 |
| Not aligned: | 2,723,408 |
Reads genomic origin
| Exonic: | 72,638,903 / 87.3% |
| Intronic: | 6,723,580 / 8.08% |
| Intergenic: | 3,847,127 / 4.62% |
| Intronic/intergenic overlapping exon: | 2,866,888 / 3.45% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.79 |
Junction analysis
| Reads at junctions: | 21,157,869 |
| ACCT | 5.38% |
| AGGT | 4.54% |
| ATCT | 3.57% |
| TCCT | 3.43% |
| GCCT | 3.41% |
| AGGA | 3.4% |
| AGCT | 2.72% |
| CCCT | 2.47% |
| AGGC | 2.42% |
| TTCT | 2.36% |
| AGAT | 2.16% |
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