Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:27:48 GMT 2023 |
| BAM file: | SRX7354202.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): | 39,847,832 / 39,815,823 |
| Number of aligned pairs (without duplicates): | 39,810,983 |
| Total number of alignments: | 84,653,268 |
| Number of secondary alignments: | 4,989,613 |
| Number of non-unique alignments: | 8,406,337 |
| Aligned to genes: | 69,070,285 |
| Ambiguous alignments: | 248,188 |
| No feature assigned: | 6,615,683 |
| Missing chromosome in annotation: | 312,775 |
| Not aligned: | 5,957,627 |
Reads genomic origin
| Exonic: | 69,070,285 / 91.26% |
| Intronic: | 3,632,231 / 4.8% |
| Intergenic: | 2,983,452 / 3.94% |
| Intronic/intergenic overlapping exon: | 2,537,455 / 3.35% |
Transcript coverage profile
| 5' bias: | 0.32 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.93 |
Junction analysis
| Reads at junctions: | 21,507,510 |
| ACCT | 5.44% |
| AGGT | 4.7% |
| TCCT | 3.66% |
| ATCT | 3.63% |
| AGGA | 3.36% |
| GCCT | 3.21% |
| AGCT | 2.64% |
| AGGC | 2.43% |
| CCCT | 2.42% |
| TTCT | 2.14% |
| AGAT | 2.06% |
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