Input data and parameters
Input
| Analysis date: | Tue Oct 31 10:01:17 GMT 2023 |
| BAM file: | SRX7354381.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): | 29,014,694 / 28,986,770 |
| Number of aligned pairs (without duplicates): | 28,982,148 |
| Total number of alignments: | 62,474,425 |
| Number of secondary alignments: | 4,472,961 |
| Number of non-unique alignments: | 6,864,462 |
| Aligned to genes: | 48,071,927 |
| Ambiguous alignments: | 180,159 |
| No feature assigned: | 6,788,576 |
| Missing chromosome in annotation: | 569,301 |
| Not aligned: | 3,511,822 |
Reads genomic origin
| Exonic: | 48,071,927 / 87.63% |
| Intronic: | 4,836,409 / 8.82% |
| Intergenic: | 1,952,167 / 3.56% |
| Intronic/intergenic overlapping exon: | 1,859,761 / 3.39% |
Transcript coverage profile
| 5' bias: | 0.34 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2 |
Junction analysis
| Reads at junctions: | 16,035,036 |
| ACCT | 5.52% |
| AGGT | 4.65% |
| ATCT | 3.59% |
| AGGA | 3.49% |
| TCCT | 3.44% |
| GCCT | 3.24% |
| AGCT | 2.74% |
| CCCT | 2.43% |
| AGGC | 2.37% |
| AGAT | 2.19% |
| TTCT | 2.13% |
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