Input data and parameters
Input
Analysis date: | Tue Oct 31 15:38:32 GMT 2023 |
BAM file: | SRX7354365.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): | 33,042,844 / 32,998,712 |
Number of aligned pairs (without duplicates): | 32,994,763 |
Total number of alignments: | 71,436,516 |
Number of secondary alignments: | 5,394,960 |
Number of non-unique alignments: | 9,233,275 |
Aligned to genes: | 55,428,180 |
Ambiguous alignments: | 188,446 |
No feature assigned: | 6,265,686 |
Missing chromosome in annotation: | 320,929 |
Not aligned: | 6,163,986 |
Reads genomic origin
Exonic: | 55,428,180 / 89.84% |
Intronic: | 3,147,593 / 5.1% |
Intergenic: | 3,118,093 / 5.05% |
Intronic/intergenic overlapping exon: | 1,917,589 / 3.11% |
Transcript coverage profile
5' bias: | 0.26 |
3' bias: | 0.21 |
5'-3' bias: | 1.95 |
Junction analysis
Reads at junctions: | 16,378,852 |
ACCT | 5.51% |
AGGT | 4.52% |
ATCT | 4.46% |
TCCT | 3.66% |
GCCT | 3.48% |
AGGA | 3.27% |
CCCT | 2.8% |
AGCT | 2.46% |
TTCT | 2.37% |
AGGC | 2.28% |
AGAT | 1.97% |