Input data and parameters
Input
| Analysis date: | Tue Oct 31 01:22:45 GMT 2023 |
| BAM file: | SRX7354368.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): | 37,170,428 / 37,141,768 |
| Number of aligned pairs (without duplicates): | 37,136,460 |
| Total number of alignments: | 79,811,499 |
| Number of secondary alignments: | 5,499,303 |
| Number of non-unique alignments: | 8,850,688 |
| Aligned to genes: | 59,896,902 |
| Ambiguous alignments: | 241,323 |
| No feature assigned: | 10,393,799 |
| Missing chromosome in annotation: | 428,787 |
| Not aligned: | 3,059,134 |
Reads genomic origin
| Exonic: | 59,896,902 / 85.21% |
| Intronic: | 7,411,119 / 10.54% |
| Intergenic: | 2,982,680 / 4.24% |
| Intronic/intergenic overlapping exon: | 2,348,760 / 3.34% |
Transcript coverage profile
| 5' bias: | 0.5 |
| 3' bias: | 0.23 |
| 5'-3' bias: | 1.96 |
Junction analysis
| Reads at junctions: | 21,483,991 |
| ACCT | 5.37% |
| AGGT | 4.65% |
| AGGA | 3.53% |
| ATCT | 3.51% |
| TCCT | 3.41% |
| GCCT | 2.8% |
| AGCT | 2.75% |
| TTCT | 2.4% |
| CCCT | 2.37% |
| AGGC | 2.35% |
| AGAT | 2.34% |
.png)
.png)
.png)
