Input data and parameters
Input
| Analysis date: | Mon Oct 30 11:20:41 GMT 2023 |
| BAM file: | SRX7354194.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): | 35,487,047 / 35,466,496 |
| Number of aligned pairs (without duplicates): | 35,463,211 |
| Total number of alignments: | 75,429,033 |
| Number of secondary alignments: | 4,475,490 |
| Number of non-unique alignments: | 7,513,282 |
| Aligned to genes: | 60,009,512 |
| Ambiguous alignments: | 196,428 |
| No feature assigned: | 7,390,473 |
| Missing chromosome in annotation: | 319,338 |
| Not aligned: | 4,749,257 |
Reads genomic origin
| Exonic: | 60,009,512 / 89.03% |
| Intronic: | 4,372,054 / 6.49% |
| Intergenic: | 3,018,419 / 4.48% |
| Intronic/intergenic overlapping exon: | 2,134,930 / 3.17% |
Transcript coverage profile
| 5' bias: | 0.32 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 2.28 |
Junction analysis
| Reads at junctions: | 17,821,940 |
| ACCT | 5.44% |
| AGGT | 4.81% |
| AGGA | 3.71% |
| ATCT | 3.66% |
| TCCT | 3.5% |
| GCCT | 2.98% |
| AGCT | 2.71% |
| AGGC | 2.41% |
| CCCT | 2.37% |
| AGAT | 2.35% |
| TTCT | 2.09% |
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