Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:46:28 GMT 2023 |
| BAM file: | SRX7354065.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): | 32,712,900 / 32,684,729 |
| Number of aligned pairs (without duplicates): | 32,677,521 |
| Total number of alignments: | 70,794,072 |
| Number of secondary alignments: | 5,396,443 |
| Number of non-unique alignments: | 8,255,744 |
| Aligned to genes: | 55,185,983 |
| Ambiguous alignments: | 226,148 |
| No feature assigned: | 6,438,792 |
| Missing chromosome in annotation: | 687,405 |
| Not aligned: | 5,318,069 |
Reads genomic origin
| Exonic: | 55,185,983 / 89.55% |
| Intronic: | 3,242,435 / 5.26% |
| Intergenic: | 3,196,357 / 5.19% |
| Intronic/intergenic overlapping exon: | 2,250,811 / 3.65% |
Transcript coverage profile
| 5' bias: | 0.15 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 1.95 |
Junction analysis
| Reads at junctions: | 18,471,170 |
| ACCT | 5.53% |
| TCCT | 5.39% |
| ATCT | 4.95% |
| AGGT | 4.06% |
| CCCT | 3.58% |
| GCCT | 2.93% |
| AGGA | 2.83% |
| TTCT | 2.37% |
| GTCT | 2.14% |
| AGGC | 2.03% |
| AGCT | 1.96% |
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