Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:19:50 GMT 2023 |
| BAM file: | SRX7354318.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): | 52,502,071 / 52,458,507 |
| Number of aligned pairs (without duplicates): | 52,441,709 |
| Total number of alignments: | 115,565,285 |
| Number of secondary alignments: | 10,604,707 |
| Number of non-unique alignments: | 16,821,063 |
| Aligned to genes: | 88,349,820 |
| Ambiguous alignments: | 386,456 |
| No feature assigned: | 8,902,341 |
| Missing chromosome in annotation: | 1,105,605 |
| Not aligned: | 3,468,956 |
Reads genomic origin
| Exonic: | 88,349,820 / 90.85% |
| Intronic: | 4,775,809 / 4.91% |
| Intergenic: | 4,126,532 / 4.24% |
| Intronic/intergenic overlapping exon: | 3,990,766 / 4.1% |
Transcript coverage profile
| 5' bias: | 0.08 |
| 3' bias: | 0.12 |
| 5'-3' bias: | 2.02 |
Junction analysis
| Reads at junctions: | 29,041,321 |
| TCCT | 6.42% |
| ACCT | 5.13% |
| ATCT | 4.69% |
| AGGT | 3.96% |
| CCCT | 3.88% |
| AGGA | 2.76% |
| GCCT | 2.33% |
| GTCT | 2.24% |
| AGGC | 2.23% |
| TTCT | 2.18% |
| TCCC | 2.07% |
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