Input data and parameters
Input
| Analysis date: | Tue Oct 31 09:16:57 GMT 2023 |
| BAM file: | SRX7354323.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): | 36,019,904 / 35,981,957 |
| Number of aligned pairs (without duplicates): | 35,977,352 |
| Total number of alignments: | 77,028,351 |
| Number of secondary alignments: | 5,026,490 |
| Number of non-unique alignments: | 8,620,465 |
| Aligned to genes: | 58,961,636 |
| Ambiguous alignments: | 207,409 |
| No feature assigned: | 8,971,461 |
| Missing chromosome in annotation: | 267,380 |
| Not aligned: | 7,788,733 |
Reads genomic origin
| Exonic: | 58,961,636 / 86.79% |
| Intronic: | 6,153,327 / 9.06% |
| Intergenic: | 2,818,134 / 4.15% |
| Intronic/intergenic overlapping exon: | 2,577,411 / 3.79% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.2 |
| 5'-3' bias: | 1.98 |
Junction analysis
| Reads at junctions: | 22,293,640 |
| ACCT | 5.55% |
| AGGT | 4.68% |
| ATCT | 3.65% |
| AGGA | 3.47% |
| GCCT | 3.36% |
| TCCT | 3.34% |
| AGCT | 2.66% |
| AGGC | 2.38% |
| CCCT | 2.37% |
| AGAT | 2.25% |
| TTCT | 2.11% |
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