Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:25:05 GMT 2023 |
| BAM file: | SRX7354125.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): | 33,148,599 / 33,119,413 |
| Number of aligned pairs (without duplicates): | 33,115,303 |
| Total number of alignments: | 70,490,484 |
| Number of secondary alignments: | 4,222,472 |
| Number of non-unique alignments: | 6,977,656 |
| Aligned to genes: | 55,242,940 |
| Ambiguous alignments: | 223,402 |
| No feature assigned: | 7,745,307 |
| Missing chromosome in annotation: | 301,179 |
| Not aligned: | 7,596,120 |
Reads genomic origin
| Exonic: | 55,242,940 / 87.7% |
| Intronic: | 5,167,106 / 8.2% |
| Intergenic: | 2,578,201 / 4.09% |
| Intronic/intergenic overlapping exon: | 2,155,217 / 3.42% |
Transcript coverage profile
| 5' bias: | 0.39 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 2 |
Junction analysis
| Reads at junctions: | 19,262,918 |
| ACCT | 5.32% |
| AGGT | 4.9% |
| ATCT | 3.63% |
| AGGA | 3.51% |
| TCCT | 3.44% |
| GCCT | 3.1% |
| AGCT | 2.79% |
| CCCT | 2.53% |
| AGGC | 2.48% |
| AGAT | 2.13% |
| TTCT | 2.07% |
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