Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:51:18 GMT 2023 |
| BAM file: | SRX7354162.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): | 43,287,942 / 43,257,926 |
| Number of aligned pairs (without duplicates): | 43,247,963 |
| Total number of alignments: | 95,645,390 |
| Number of secondary alignments: | 9,099,522 |
| Number of non-unique alignments: | 13,734,213 |
| Aligned to genes: | 72,355,230 |
| Ambiguous alignments: | 340,285 |
| No feature assigned: | 7,825,609 |
| Missing chromosome in annotation: | 1,390,053 |
| Not aligned: | 3,586,752 |
Reads genomic origin
| Exonic: | 72,355,230 / 90.24% |
| Intronic: | 4,258,933 / 5.31% |
| Intergenic: | 3,566,676 / 4.45% |
| Intronic/intergenic overlapping exon: | 3,968,671 / 4.95% |
Transcript coverage profile
| 5' bias: | 0.07 |
| 3' bias: | 0.1 |
| 5'-3' bias: | 2.27 |
Junction analysis
| Reads at junctions: | 20,651,047 |
| TCCT | 5.65% |
| ACCT | 5.1% |
| ATCT | 4.55% |
| CCCT | 4.54% |
| AGGT | 4.19% |
| AGGA | 2.74% |
| AGGC | 2.27% |
| GCCT | 2.15% |
| GTCT | 2.13% |
| TTCT | 2.07% |
| AGAC | 1.89% |
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