Input data and parameters
Input
Analysis date: | Sun Oct 29 01:57:57 GMT 2023 |
BAM file: | SRX7354109.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): | 45,462,120 / 45,413,785 |
Number of aligned pairs (without duplicates): | 45,401,913 |
Total number of alignments: | 96,206,842 |
Number of secondary alignments: | 5,330,937 |
Number of non-unique alignments: | 8,757,011 |
Aligned to genes: | 75,424,820 |
Ambiguous alignments: | 236,025 |
No feature assigned: | 11,338,793 |
Missing chromosome in annotation: | 450,193 |
Not aligned: | 8,587,413 |
Reads genomic origin
Exonic: | 75,424,820 / 86.93% |
Intronic: | 6,582,804 / 7.59% |
Intergenic: | 4,755,989 / 5.48% |
Intronic/intergenic overlapping exon: | 3,386,627 / 3.9% |
Transcript coverage profile
5' bias: | 0.28 |
3' bias: | 0.16 |
5'-3' bias: | 1.78 |
Junction analysis
Reads at junctions: | 23,191,804 |
ACCT | 5.2% |
AGGT | 4.69% |
ATCT | 3.68% |
AGGA | 3.66% |
TCCT | 3.33% |
GCCT | 3.07% |
AGCT | 2.84% |
AGGC | 2.37% |
CCCT | 2.37% |
AGAT | 2.28% |
TTCT | 2.21% |