Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:35:43 GMT 2023 |
| BAM file: | SRX7354140.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): | 103,680,630 / 103,557,076 |
| Number of aligned pairs (without duplicates): | 103,538,379 |
| Total number of alignments: | 221,428,415 |
| Number of secondary alignments: | 14,190,709 |
| Number of non-unique alignments: | 23,931,912 |
| Aligned to genes: | 171,102,614 |
| Ambiguous alignments: | 650,177 |
| No feature assigned: | 24,801,147 |
| Missing chromosome in annotation: | 942,565 |
| Not aligned: | 6,840,020 |
Reads genomic origin
| Exonic: | 171,102,614 / 87.34% |
| Intronic: | 16,858,786 / 8.61% |
| Intergenic: | 7,942,361 / 4.05% |
| Intronic/intergenic overlapping exon: | 7,689,064 / 3.92% |
Transcript coverage profile
| 5' bias: | 0.45 |
| 3' bias: | 0.22 |
| 5'-3' bias: | 1.81 |
Junction analysis
| Reads at junctions: | 56,212,798 |
| ACCT | 5.17% |
| AGGT | 4.88% |
| AGGA | 3.6% |
| TCCT | 3.47% |
| ATCT | 3.43% |
| GCCT | 3.01% |
| AGCT | 2.76% |
| CCCT | 2.62% |
| AGGC | 2.54% |
| AGAT | 2.32% |
| TTCT | 2.23% |

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