Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:33:19 GMT 2023 |
| BAM file: | SRX7354135.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): | 32,907,421 / 32,881,427 |
| Number of aligned pairs (without duplicates): | 32,877,541 |
| Total number of alignments: | 69,879,120 |
| Number of secondary alignments: | 4,090,272 |
| Number of non-unique alignments: | 6,767,039 |
| Aligned to genes: | 54,390,617 |
| Ambiguous alignments: | 186,582 |
| No feature assigned: | 8,221,258 |
| Missing chromosome in annotation: | 313,624 |
| Not aligned: | 5,995,000 |
Reads genomic origin
| Exonic: | 54,390,617 / 86.87% |
| Intronic: | 5,504,175 / 8.79% |
| Intergenic: | 2,717,083 / 4.34% |
| Intronic/intergenic overlapping exon: | 2,218,566 / 3.54% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.89 |
Junction analysis
| Reads at junctions: | 17,881,100 |
| ACCT | 5.33% |
| AGGT | 4.74% |
| ATCT | 3.62% |
| AGGA | 3.58% |
| TCCT | 3.55% |
| GCCT | 3.2% |
| AGCT | 2.73% |
| CCCT | 2.52% |
| AGGC | 2.38% |
| AGAT | 2.28% |
| TTCT | 2.1% |

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