Input data and parameters
Input
| Analysis date: | Mon Oct 30 20:21:35 GMT 2023 |
| BAM file: | SRX7354231.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): | 38,119,584 / 38,089,682 |
| Number of aligned pairs (without duplicates): | 38,086,376 |
| Total number of alignments: | 81,282,086 |
| Number of secondary alignments: | 5,072,820 |
| Number of non-unique alignments: | 8,301,638 |
| Aligned to genes: | 63,716,105 |
| Ambiguous alignments: | 237,206 |
| No feature assigned: | 8,683,383 |
| Missing chromosome in annotation: | 343,754 |
| Not aligned: | 5,145,444 |
Reads genomic origin
| Exonic: | 63,716,105 / 88.01% |
| Intronic: | 5,893,560 / 8.14% |
| Intergenic: | 2,789,823 / 3.85% |
| Intronic/intergenic overlapping exon: | 2,295,159 / 3.17% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.18 |
| 5'-3' bias: | 2 |
Junction analysis
| Reads at junctions: | 23,099,454 |
| ACCT | 5.66% |
| AGGT | 4.83% |
| AGGA | 3.77% |
| TCCT | 3.46% |
| ATCT | 3.43% |
| GCCT | 2.89% |
| AGCT | 2.82% |
| AGGC | 2.46% |
| AGAT | 2.44% |
| CCCT | 2.38% |
| TTCT | 2.24% |
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