Input data and parameters
Input
| Analysis date: | Sun Oct 29 01:57:44 GMT 2023 |
| BAM file: | SRX7354099.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): | 32,739,446 / 32,707,132 |
| Number of aligned pairs (without duplicates): | 32,701,198 |
| Total number of alignments: | 69,858,176 |
| Number of secondary alignments: | 4,411,598 |
| Number of non-unique alignments: | 6,989,813 |
| Aligned to genes: | 56,402,585 |
| Ambiguous alignments: | 215,522 |
| No feature assigned: | 5,862,154 |
| Missing chromosome in annotation: | 388,102 |
| Not aligned: | 4,158,452 |
Reads genomic origin
| Exonic: | 56,402,585 / 90.59% |
| Intronic: | 3,593,741 / 5.77% |
| Intergenic: | 2,268,413 / 3.64% |
| Intronic/intergenic overlapping exon: | 2,195,794 / 3.53% |
Transcript coverage profile
| 5' bias: | 0.13 |
| 3' bias: | 0.16 |
| 5'-3' bias: | 2.05 |
Junction analysis
| Reads at junctions: | 17,886,348 |
| ATCT | 5.08% |
| ACCT | 4.81% |
| TCCT | 4.62% |
| AGGT | 4.48% |
| CCCT | 3.55% |
| AGGA | 3.04% |
| GCCT | 2.62% |
| TTCT | 2.42% |
| AGCT | 2.12% |
| AGGC | 2.08% |
| AGAA | 1.96% |

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