Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:46:15 GMT 2023 |
| BAM file: | SRX7354172.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): | 31,107,863 / 31,086,424 |
| Number of aligned pairs (without duplicates): | 31,082,532 |
| Total number of alignments: | 65,994,299 |
| Number of secondary alignments: | 3,800,012 |
| Number of non-unique alignments: | 6,251,368 |
| Aligned to genes: | 51,897,122 |
| Ambiguous alignments: | 175,611 |
| No feature assigned: | 7,350,117 |
| Missing chromosome in annotation: | 320,081 |
| Not aligned: | 3,049,015 |
Reads genomic origin
| Exonic: | 51,897,122 / 87.59% |
| Intronic: | 4,787,409 / 8.08% |
| Intergenic: | 2,562,708 / 4.33% |
| Intronic/intergenic overlapping exon: | 2,136,688 / 3.61% |
Transcript coverage profile
| 5' bias: | 0.38 |
| 3' bias: | 0.19 |
| 5'-3' bias: | 2.17 |
Junction analysis
| Reads at junctions: | 15,742,232 |
| ACCT | 5.47% |
| AGGT | 4.76% |
| ATCT | 3.71% |
| AGGA | 3.54% |
| TCCT | 3.49% |
| GCCT | 3.08% |
| AGCT | 2.71% |
| CCCT | 2.45% |
| AGGC | 2.36% |
| AGAT | 2.21% |
| TTCT | 2.1% |
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