Input data and parameters
Input
| Analysis date: | Mon Oct 30 19:44:14 GMT 2023 |
| BAM file: | SRX7354225.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): | 44,234,746 / 44,210,880 |
| Number of aligned pairs (without duplicates): | 44,206,827 |
| Total number of alignments: | 93,544,680 |
| Number of secondary alignments: | 5,099,054 |
| Number of non-unique alignments: | 8,442,016 |
| Aligned to genes: | 74,519,159 |
| Ambiguous alignments: | 280,473 |
| No feature assigned: | 9,917,955 |
| Missing chromosome in annotation: | 385,077 |
| Not aligned: | 1,869,158 |
Reads genomic origin
| Exonic: | 74,519,159 / 88.25% |
| Intronic: | 5,910,718 / 7% |
| Intergenic: | 4,007,237 / 4.75% |
| Intronic/intergenic overlapping exon: | 3,165,349 / 3.75% |
Transcript coverage profile
| 5' bias: | 0.4 |
| 3' bias: | 0.25 |
| 5'-3' bias: | 1.72 |
Junction analysis
| Reads at junctions: | 28,864,540 |
| ACCT | 5.41% |
| AGGT | 4.58% |
| TCCT | 3.76% |
| ATCT | 3.65% |
| GCCT | 3.65% |
| AGGA | 3.08% |
| AGCT | 2.56% |
| CCCT | 2.5% |
| AGGC | 2.45% |
| TTCT | 2.24% |
| TCCC | 2.04% |
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