Input data and parameters 

Input

Analysis date: Mon Oct 30 23:28:07 GMT 2023
BAM file: SRX7354289.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): 52,631,495 / 52,605,509
Number of aligned pairs (without duplicates): 52,594,053
Total number of alignments: 113,718,970
Number of secondary alignments: 8,481,966
Number of non-unique alignments: 13,419,243
Aligned to genes: 90,554,612
Ambiguous alignments: 393,234
No feature assigned: 8,391,253
Missing chromosome in annotation: 960,628
Not aligned: 2,217,064

Reads genomic origin

Exonic: 90,554,612 / 91.52%
Intronic: 4,241,051 / 4.29%
Intergenic: 4,150,202 / 4.19%
Intronic/intergenic overlapping exon: 3,535,554 / 3.57%

Transcript coverage profile

5' bias: 0.1
3' bias: 0.14
5'-3' bias: 2.06

Junction analysis

Reads at junctions: 23,820,891
ACCT 4.85%
AGGT 4.59%
TCCT 4.41%
ATCT 4.22%
CCCT 3.47%
AGGA 3.32%
AGGC 2.36%
AGCT 2.13%
GCCT 2.13%
TTCT 1.97%
AGAC 1.84%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis