Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:53:13 GMT 2023 |
| BAM file: | SRX7354136.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): | 42,863,891 / 42,823,200 |
| Number of aligned pairs (without duplicates): | 42,817,518 |
| Total number of alignments: | 90,759,587 |
| Number of secondary alignments: | 5,072,496 |
| Number of non-unique alignments: | 8,584,494 |
| Aligned to genes: | 73,206,486 |
| Ambiguous alignments: | 257,821 |
| No feature assigned: | 8,427,612 |
| Missing chromosome in annotation: | 283,174 |
| Not aligned: | 8,308,007 |
Reads genomic origin
| Exonic: | 73,206,486 / 89.68% |
| Intronic: | 4,991,353 / 6.11% |
| Intergenic: | 3,436,259 / 4.21% |
| Intronic/intergenic overlapping exon: | 2,800,341 / 3.43% |
Transcript coverage profile
| 5' bias: | 0.3 |
| 3' bias: | 0.17 |
| 5'-3' bias: | 1.93 |
Junction analysis
| Reads at junctions: | 24,213,419 |
| ACCT | 5.43% |
| AGGT | 4.63% |
| ATCT | 3.65% |
| TCCT | 3.48% |
| AGGA | 3.42% |
| GCCT | 3.36% |
| AGCT | 2.67% |
| AGGC | 2.47% |
| CCCT | 2.34% |
| AGAT | 2.15% |
| TTCT | 2.12% |
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