Input data and parameters
Input
| Analysis date: | Tue Oct 31 13:20:37 GMT 2023 |
| BAM file: | SRX7354405.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): | 30,763,113 / 30,730,289 |
| Number of aligned pairs (without duplicates): | 30,725,787 |
| Total number of alignments: | 65,867,973 |
| Number of secondary alignments: | 4,374,571 |
| Number of non-unique alignments: | 7,355,850 |
| Aligned to genes: | 52,712,121 |
| Ambiguous alignments: | 188,842 |
| No feature assigned: | 5,326,374 |
| Missing chromosome in annotation: | 284,786 |
| Not aligned: | 9,694,352 |
Reads genomic origin
| Exonic: | 52,712,121 / 90.82% |
| Intronic: | 3,204,950 / 5.52% |
| Intergenic: | 2,121,424 / 3.66% |
| Intronic/intergenic overlapping exon: | 1,751,488 / 3.02% |
Transcript coverage profile
| 5' bias: | 0.28 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2.12 |
Junction analysis
| Reads at junctions: | 17,360,014 |
| ACCT | 5.37% |
| AGGT | 4.53% |
| ATCT | 3.78% |
| TCCT | 3.58% |
| AGGA | 3.35% |
| GCCT | 3.11% |
| AGCT | 2.55% |
| CCCT | 2.45% |
| AGGC | 2.34% |
| AGGG | 2.15% |
| TTCT | 2.02% |
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