Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:44:22 GMT 2023 |
| BAM file: | SRX7354106.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): | 39,810,507 / 39,756,827 |
| Number of aligned pairs (without duplicates): | 39,748,364 |
| Total number of alignments: | 85,246,390 |
| Number of secondary alignments: | 5,679,056 |
| Number of non-unique alignments: | 9,062,760 |
| Aligned to genes: | 66,122,623 |
| Ambiguous alignments: | 291,438 |
| No feature assigned: | 9,241,341 |
| Missing chromosome in annotation: | 528,228 |
| Not aligned: | 2,190,528 |
Reads genomic origin
| Exonic: | 66,122,623 / 87.74% |
| Intronic: | 6,780,137 / 9% |
| Intergenic: | 2,461,204 / 3.27% |
| Intronic/intergenic overlapping exon: | 4,248,179 / 5.64% |
Transcript coverage profile
| 5' bias: | 0.26 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 1.87 |
Junction analysis
| Reads at junctions: | 26,659,668 |
| ACCT | 5.59% |
| AGGT | 4.42% |
| TCCT | 4.39% |
| ATCT | 4.33% |
| GCCT | 3.54% |
| CCCT | 2.99% |
| AGGA | 2.97% |
| AGGC | 2.3% |
| AGCT | 2.28% |
| TCCC | 2.16% |
| TTCT | 2.13% |
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