Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:19:17 GMT 2023 |
| BAM file: | SRX7354108.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): | 44,274,461 / 44,246,543 |
| Number of aligned pairs (without duplicates): | 44,240,878 |
| Total number of alignments: | 95,743,417 |
| Number of secondary alignments: | 7,222,413 |
| Number of non-unique alignments: | 10,808,642 |
| Aligned to genes: | 73,419,021 |
| Ambiguous alignments: | 314,130 |
| No feature assigned: | 10,102,820 |
| Missing chromosome in annotation: | 1,098,804 |
| Not aligned: | 2,139,304 |
Reads genomic origin
| Exonic: | 73,419,021 / 87.9% |
| Intronic: | 7,539,952 / 9.03% |
| Intergenic: | 2,562,868 / 3.07% |
| Intronic/intergenic overlapping exon: | 3,333,188 / 3.99% |
Transcript coverage profile
| 5' bias: | 0.3 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 1.62 |
Junction analysis
| Reads at junctions: | 24,174,681 |
| ACCT | 5.26% |
| AGGT | 4.66% |
| ATCT | 3.8% |
| TCCT | 3.69% |
| GCCT | 3.4% |
| AGGA | 3.36% |
| CCCT | 2.68% |
| AGCT | 2.65% |
| AGGC | 2.42% |
| TTCT | 2.11% |
| AGAT | 2.1% |
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