Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:12:58 GMT 2023 |
| BAM file: | SRX7354244.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): | 18,291,837 / 18,281,733 |
| Number of aligned pairs (without duplicates): | 18,280,040 |
| Total number of alignments: | 38,943,229 |
| Number of secondary alignments: | 2,369,659 |
| Number of non-unique alignments: | 3,890,389 |
| Aligned to genes: | 30,311,160 |
| Ambiguous alignments: | 110,610 |
| No feature assigned: | 4,449,287 |
| Missing chromosome in annotation: | 181,783 |
| Not aligned: | 1,687,854 |
Reads genomic origin
| Exonic: | 30,311,160 / 87.2% |
| Intronic: | 3,104,436 / 8.93% |
| Intergenic: | 1,344,851 / 3.87% |
| Intronic/intergenic overlapping exon: | 1,164,664 / 3.35% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2.2 |
Junction analysis
| Reads at junctions: | 10,310,923 |
| ACCT | 5.27% |
| AGGT | 4.7% |
| TCCT | 3.61% |
| ATCT | 3.56% |
| AGGA | 3.55% |
| GCCT | 2.94% |
| AGCT | 2.7% |
| CCCT | 2.45% |
| AGGC | 2.41% |
| AGAT | 2.23% |
| TTCT | 2.13% |
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