Input data and parameters
Input
Analysis date: | Tue Oct 31 17:17:45 GMT 2023 |
BAM file: | SRX7354408.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): | 35,615,661 / 35,584,685 |
Number of aligned pairs (without duplicates): | 35,581,893 |
Total number of alignments: | 75,220,298 |
Number of secondary alignments: | 4,019,952 |
Number of non-unique alignments: | 6,836,677 |
Aligned to genes: | 59,595,720 |
Ambiguous alignments: | 198,524 |
No feature assigned: | 8,359,462 |
Missing chromosome in annotation: | 229,915 |
Not aligned: | 4,317,470 |
Reads genomic origin
Exonic: | 59,595,720 / 87.7% |
Intronic: | 5,676,197 / 8.35% |
Intergenic: | 2,683,265 / 3.95% |
Intronic/intergenic overlapping exon: | 2,278,206 / 3.35% |
Transcript coverage profile
5' bias: | 0.34 |
3' bias: | 0.18 |
5'-3' bias: | 1.94 |
Junction analysis
Reads at junctions: | 19,615,740 |
ACCT | 5.52% |
AGGT | 4.69% |
ATCT | 3.56% |
AGGA | 3.51% |
TCCT | 3.4% |
GCCT | 3.28% |
AGCT | 2.72% |
AGGC | 2.41% |
AGAT | 2.35% |
CCCT | 2.33% |
TTCT | 2.26% |