Input data and parameters
Input
| Analysis date: | Mon Oct 30 22:35:13 GMT 2023 |
| BAM file: | SRX7354253.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): | 30,549,913 / 30,537,413 |
| Number of aligned pairs (without duplicates): | 30,535,104 |
| Total number of alignments: | 65,375,283 |
| Number of secondary alignments: | 4,287,957 |
| Number of non-unique alignments: | 6,973,828 |
| Aligned to genes: | 51,978,879 |
| Ambiguous alignments: | 203,655 |
| No feature assigned: | 5,863,617 |
| Missing chromosome in annotation: | 355,304 |
| Not aligned: | 1,130,136 |
Reads genomic origin
| Exonic: | 51,978,879 / 89.86% |
| Intronic: | 3,931,028 / 6.8% |
| Intergenic: | 1,932,589 / 3.34% |
| Intronic/intergenic overlapping exon: | 1,689,528 / 2.92% |
Transcript coverage profile
| 5' bias: | 0.37 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.97 |
Junction analysis
| Reads at junctions: | 17,452,726 |
| ACCT | 5.42% |
| AGGT | 4.65% |
| ATCT | 3.6% |
| AGGA | 3.52% |
| TCCT | 3.48% |
| GCCT | 3.37% |
| AGCT | 2.61% |
| CCCT | 2.41% |
| AGGC | 2.35% |
| AGAT | 2.27% |
| TTCT | 2.18% |
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