Input data and parameters 

Input

Analysis date: Mon Oct 30 20:19:11 GMT 2023
BAM file: SRX7354236.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): 36,441,553 / 36,427,076
Number of aligned pairs (without duplicates): 36,424,031
Total number of alignments: 77,365,448
Number of secondary alignments: 4,496,819
Number of non-unique alignments: 7,589,668
Aligned to genes: 61,923,542
Ambiguous alignments: 222,453
No feature assigned: 7,369,929
Missing chromosome in annotation: 259,856
Not aligned: 2,743,845

Reads genomic origin

Exonic: 61,923,542 / 89.36%
Intronic: 4,815,420 / 6.95%
Intergenic: 2,554,509 / 3.69%
Intronic/intergenic overlapping exon: 2,098,652 / 3.03%

Transcript coverage profile

5' bias: 0.29
3' bias: 0.18
5'-3' bias: 2.1

Junction analysis

Reads at junctions: 20,132,021
ACCT 5.36%
AGGT 4.9%
ATCT 3.79%
AGGA 3.65%
TCCT 3.56%
GCCT 2.95%
AGCT 2.77%
CCCT 2.5%
AGGC 2.38%
AGAT 2.32%
TTCT 2.18%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis