Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:11:57 GMT 2023 |
| BAM file: | SRX7354101.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): | 30,575,032 / 30,474,505 |
| Number of aligned pairs (without duplicates): | 30,460,099 |
| Total number of alignments: | 64,880,934 |
| Number of secondary alignments: | 3,831,397 |
| Number of non-unique alignments: | 6,518,319 |
| Aligned to genes: | 50,875,929 |
| Ambiguous alignments: | 185,694 |
| No feature assigned: | 7,129,641 |
| Missing chromosome in annotation: | 171,351 |
| Not aligned: | 11,590,159 |
Reads genomic origin
| Exonic: | 50,875,929 / 87.71% |
| Intronic: | 4,139,631 / 7.14% |
| Intergenic: | 2,990,010 / 5.15% |
| Intronic/intergenic overlapping exon: | 2,042,604 / 3.52% |
Transcript coverage profile
| 5' bias: | 0.28 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 2.36 |
Junction analysis
| Reads at junctions: | 16,141,318 |
| ACCT | 5.7% |
| AGGT | 4.73% |
| ATCT | 3.8% |
| TCCT | 3.72% |
| AGGA | 3.46% |
| GCCT | 3.16% |
| CCCT | 2.58% |
| AGCT | 2.51% |
| AGGC | 2.32% |
| AGAT | 2.1% |
| TTCT | 2.06% |
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