Input data and parameters
Input
| Analysis date: | Tue Oct 31 18:04:17 GMT 2023 |
| BAM file: | SRX7354347.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): | 52,167,326 / 52,125,885 |
| Number of aligned pairs (without duplicates): | 52,113,449 |
| Total number of alignments: | 134,902,063 |
| Number of secondary alignments: | 30,608,852 |
| Number of non-unique alignments: | 25,019,849 |
| Aligned to genes: | 83,252,552 |
| Ambiguous alignments: | 381,211 |
| No feature assigned: | 11,848,255 |
| Missing chromosome in annotation: | 14,400,196 |
| Not aligned: | 6,522,903 |
Reads genomic origin
| Exonic: | 83,252,552 / 87.54% |
| Intronic: | 7,746,584 / 8.15% |
| Intergenic: | 4,101,671 / 4.31% |
| Intronic/intergenic overlapping exon: | 3,642,252 / 3.83% |
Transcript coverage profile
| 5' bias: | 0.23 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 2 |
Junction analysis
| Reads at junctions: | 28,971,195 |
| ACCT | 5.45% |
| AGGT | 4.47% |
| TCCT | 4.41% |
| ATCT | 4.15% |
| CCCT | 3.25% |
| GCCT | 3.21% |
| AGGA | 3.01% |
| AGGC | 2.38% |
| AGCT | 2.21% |
| TTCT | 2.15% |
| AGAA | 1.74% |
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