Input data and parameters
Input
| Analysis date: | Sun Oct 29 11:28:00 GMT 2023 |
| BAM file: | SRX7354078.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): | 41,877,628 / 41,860,470 |
| Number of aligned pairs (without duplicates): | 41,849,209 |
| Total number of alignments: | 89,570,424 |
| Number of secondary alignments: | 5,832,326 |
| Number of non-unique alignments: | 9,407,928 |
| Aligned to genes: | 71,624,947 |
| Ambiguous alignments: | 239,266 |
| No feature assigned: | 7,744,382 |
| Missing chromosome in annotation: | 553,901 |
| Not aligned: | 2,623,862 |
Reads genomic origin
| Exonic: | 71,624,947 / 90.24% |
| Intronic: | 4,815,318 / 6.07% |
| Intergenic: | 2,929,064 / 3.69% |
| Intronic/intergenic overlapping exon: | 2,970,831 / 3.74% |
Transcript coverage profile
| 5' bias: | 0.21 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.04 |
Junction analysis
| Reads at junctions: | 22,607,454 |
| ACCT | 5.51% |
| ATCT | 4.43% |
| AGGT | 4.4% |
| TCCT | 4.01% |
| GCCT | 3.44% |
| AGGA | 3.14% |
| CCCT | 2.67% |
| AGCT | 2.26% |
| AGGC | 2.18% |
| TTCT | 2.1% |
| TCCC | 2.03% |
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