Input data and parameters
Input
Analysis date: | Mon Oct 30 12:46:59 GMT 2023 |
BAM file: | SRX7354212.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): | 37,942,763 / 37,933,733 |
Number of aligned pairs (without duplicates): | 37,930,542 |
Total number of alignments: | 80,868,024 |
Number of secondary alignments: | 4,991,528 |
Number of non-unique alignments: | 8,258,805 |
Aligned to genes: | 63,934,321 |
Ambiguous alignments: | 214,149 |
No feature assigned: | 8,095,208 |
Missing chromosome in annotation: | 365,541 |
Not aligned: | 1,442,106 |
Reads genomic origin
Exonic: | 63,934,321 / 88.76% |
Intronic: | 5,163,269 / 7.17% |
Intergenic: | 2,931,939 / 4.07% |
Intronic/intergenic overlapping exon: | 2,154,000 / 2.99% |
Transcript coverage profile
5' bias: | 0.32 |
3' bias: | 0.17 |
5'-3' bias: | 2.02 |
Junction analysis
Reads at junctions: | 19,757,900 |
ACCT | 5.56% |
AGGT | 4.78% |
AGGA | 3.52% |
ATCT | 3.49% |
GCCT | 3.28% |
TCCT | 3.26% |
AGCT | 2.77% |
AGGC | 2.41% |
AGAT | 2.3% |
CCCT | 2.29% |
TTCT | 2.17% |