Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:36:33 GMT 2023 |
| BAM file: | SRX7354344.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): | 38,731,464 / 38,697,306 |
| Number of aligned pairs (without duplicates): | 38,693,744 |
| Total number of alignments: | 82,525,911 |
| Number of secondary alignments: | 5,097,141 |
| Number of non-unique alignments: | 8,680,446 |
| Aligned to genes: | 65,071,975 |
| Ambiguous alignments: | 240,079 |
| No feature assigned: | 8,244,553 |
| Missing chromosome in annotation: | 288,858 |
| Not aligned: | 3,129,702 |
Reads genomic origin
| Exonic: | 65,071,975 / 88.75% |
| Intronic: | 5,229,003 / 7.13% |
| Intergenic: | 3,015,550 / 4.11% |
| Intronic/intergenic overlapping exon: | 2,409,472 / 3.29% |
Transcript coverage profile
| 5' bias: | 0.31 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.85 |
Junction analysis
| Reads at junctions: | 19,444,197 |
| ACCT | 5.34% |
| AGGT | 4.6% |
| ATCT | 3.68% |
| TCCT | 3.67% |
| AGGA | 3.46% |
| GCCT | 3.34% |
| AGCT | 2.64% |
| CCCT | 2.61% |
| AGGC | 2.44% |
| AGAT | 2.23% |
| TTCT | 2.16% |

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