Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:29:42 GMT 2023 |
| BAM file: | SRX7354139.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): | 45,552,438 / 45,501,949 |
| Number of aligned pairs (without duplicates): | 45,484,368 |
| Total number of alignments: | 100,178,578 |
| Number of secondary alignments: | 9,124,191 |
| Number of non-unique alignments: | 12,406,841 |
| Aligned to genes: | 75,484,425 |
| Ambiguous alignments: | 258,981 |
| No feature assigned: | 10,003,424 |
| Missing chromosome in annotation: | 2,024,907 |
| Not aligned: | 2,756,487 |
Reads genomic origin
| Exonic: | 75,484,425 / 88.3% |
| Intronic: | 6,365,459 / 7.45% |
| Intergenic: | 3,637,965 / 4.26% |
| Intronic/intergenic overlapping exon: | 3,619,864 / 4.23% |
Transcript coverage profile
| 5' bias: | 0.52 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.98 |
Junction analysis
| Reads at junctions: | 23,174,917 |
| ACCT | 5.1% |
| AGGT | 4.84% |
| ATCT | 3.59% |
| TCCT | 3.49% |
| AGGA | 3.42% |
| GCCT | 3.31% |
| CCCT | 2.87% |
| AGCT | 2.76% |
| AGGC | 2.52% |
| TTCT | 2.25% |
| AGAT | 2.11% |

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