Input data and parameters 

Input

Analysis date: Mon Oct 30 20:09:40 GMT 2023
BAM file: SRX7354198.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): 38,215,094 / 38,192,852
Number of aligned pairs (without duplicates): 38,190,131
Total number of alignments: 81,210,745
Number of secondary alignments: 4,802,799
Number of non-unique alignments: 8,040,508
Aligned to genes: 64,526,635
Ambiguous alignments: 215,579
No feature assigned: 8,087,077
Missing chromosome in annotation: 340,946
Not aligned: 3,218,298

Reads genomic origin

Exonic: 64,526,635 / 88.86%
Intronic: 5,282,114 / 7.27%
Intergenic: 2,804,963 / 3.86%
Intronic/intergenic overlapping exon: 2,364,879 / 3.26%

Transcript coverage profile

5' bias: 0.35
3' bias: 0.2
5'-3' bias: 2.12

Junction analysis

Reads at junctions: 20,443,792
ACCT 5.45%
AGGT 4.57%
ATCT 3.8%
TCCT 3.46%
AGGA 3.37%
GCCT 3.25%
AGCT 2.72%
TTCT 2.47%
CCCT 2.43%
AGGC 2.3%
AGAT 2.19%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis