Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:45:13 GMT 2023 |
| BAM file: | SRX7354100.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): | 42,907,737 / 42,873,796 |
| Number of aligned pairs (without duplicates): | 42,864,362 |
| Total number of alignments: | 92,994,472 |
| Number of secondary alignments: | 7,212,939 |
| Number of non-unique alignments: | 11,525,659 |
| Aligned to genes: | 73,128,212 |
| Ambiguous alignments: | 262,473 |
| No feature assigned: | 7,325,431 |
| Missing chromosome in annotation: | 752,697 |
| Not aligned: | 3,021,345 |
Reads genomic origin
| Exonic: | 73,128,212 / 90.89% |
| Intronic: | 4,641,559 / 5.77% |
| Intergenic: | 2,683,872 / 3.34% |
| Intronic/intergenic overlapping exon: | 2,656,827 / 3.3% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 1.79 |
Junction analysis
| Reads at junctions: | 22,030,480 |
| AGGT | 5.03% |
| ACCT | 5.02% |
| AGGA | 3.6% |
| TCCT | 3.6% |
| ATCT | 3.52% |
| GCCT | 2.68% |
| AGCT | 2.62% |
| AGGC | 2.47% |
| CCCT | 2.44% |
| AGAT | 2.1% |
| TTCT | 2.02% |

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