Input data and parameters
Input
| Analysis date: | Sun Oct 29 11:57:54 GMT 2023 |
| BAM file: | SRX7354143.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): | 42,420,283 / 42,408,075 |
| Number of aligned pairs (without duplicates): | 42,402,310 |
| Total number of alignments: | 90,313,194 |
| Number of secondary alignments: | 5,484,836 |
| Number of non-unique alignments: | 8,866,595 |
| Aligned to genes: | 71,504,395 |
| Ambiguous alignments: | 229,608 |
| No feature assigned: | 9,238,353 |
| Missing chromosome in annotation: | 474,243 |
| Not aligned: | 1,906,390 |
Reads genomic origin
| Exonic: | 71,504,395 / 88.56% |
| Intronic: | 6,590,273 / 8.16% |
| Intergenic: | 2,648,080 / 3.28% |
| Intronic/intergenic overlapping exon: | 3,031,823 / 3.75% |
Transcript coverage profile
| 5' bias: | 0.31 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 2.21 |
Junction analysis
| Reads at junctions: | 24,151,636 |
| ACCT | 5.47% |
| AGGT | 4.69% |
| ATCT | 3.79% |
| TCCT | 3.61% |
| AGGA | 3.5% |
| GCCT | 3.16% |
| AGCT | 2.59% |
| AGGC | 2.34% |
| CCCT | 2.31% |
| AGAT | 2.08% |
| TTCT | 2.04% |
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