Input data and parameters
Input
| Analysis date: | Sun Oct 29 13:02:07 GMT 2023 |
| BAM file: | SRX7354190.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): | 51,415,388 / 51,403,402 |
| Number of aligned pairs (without duplicates): | 51,349,523 |
| Total number of alignments: | 112,213,115 |
| Number of secondary alignments: | 9,394,325 |
| Number of non-unique alignments: | 13,576,579 |
| Aligned to genes: | 86,421,407 |
| Ambiguous alignments: | 292,615 |
| No feature assigned: | 10,220,054 |
| Missing chromosome in annotation: | 1,702,460 |
| Not aligned: | 2,526,802 |
Reads genomic origin
| Exonic: | 86,421,407 / 89.42% |
| Intronic: | 6,281,743 / 6.5% |
| Intergenic: | 3,938,311 / 4.08% |
| Intronic/intergenic overlapping exon: | 4,194,631 / 4.34% |
Transcript coverage profile
| 5' bias: | 0.39 |
| 3' bias: | 0.24 |
| 5'-3' bias: | 2.08 |
Junction analysis
| Reads at junctions: | 27,884,925 |
| ACCT | 5.22% |
| AGGT | 4.62% |
| ATCT | 4.15% |
| TCCT | 4.13% |
| AGGA | 3.25% |
| GCCT | 3.19% |
| CCCT | 3.02% |
| AGCT | 2.42% |
| TTCT | 2.31% |
| AGGC | 2.3% |
| AGAA | 1.86% |
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