Input data and parameters
Input
| Analysis date: | Tue Oct 31 13:21:54 GMT 2023 |
| BAM file: | SRX7354380.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): | 32,475,923 / 32,454,361 |
| Number of aligned pairs (without duplicates): | 32,450,754 |
| Total number of alignments: | 68,982,208 |
| Number of secondary alignments: | 4,051,924 |
| Number of non-unique alignments: | 6,742,741 |
| Aligned to genes: | 54,667,406 |
| Ambiguous alignments: | 181,723 |
| No feature assigned: | 7,130,079 |
| Missing chromosome in annotation: | 260,259 |
| Not aligned: | 3,222,682 |
Reads genomic origin
| Exonic: | 54,667,406 / 88.46% |
| Intronic: | 4,815,554 / 7.79% |
| Intergenic: | 2,314,525 / 3.75% |
| Intronic/intergenic overlapping exon: | 2,056,989 / 3.33% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.21 |
| 5'-3' bias: | 1.94 |
Junction analysis
| Reads at junctions: | 19,038,012 |
| ACCT | 5.25% |
| AGGT | 4.55% |
| ATCT | 3.56% |
| AGGA | 3.52% |
| TCCT | 3.4% |
| GCCT | 3.21% |
| AGCT | 2.88% |
| AGGC | 2.35% |
| AGAT | 2.27% |
| CCCT | 2.26% |
| TTCT | 2.08% |
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