Input data and parameters 

Input

Analysis date: Mon Oct 30 23:14:58 GMT 2023
BAM file: SRX7354282.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): 39,897,390 / 39,879,538
Number of aligned pairs (without duplicates): 39,876,251
Total number of alignments: 83,836,422
Number of secondary alignments: 4,059,494
Number of non-unique alignments: 7,027,679
Aligned to genes: 69,640,242
Ambiguous alignments: 200,633
No feature assigned: 6,774,157
Missing chromosome in annotation: 193,711
Not aligned: 2,390,252

Reads genomic origin

Exonic: 69,640,242 / 91.13%
Intronic: 3,466,300 / 4.54%
Intergenic: 3,307,857 / 4.33%
Intronic/intergenic overlapping exon: 2,444,468 / 3.2%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.13
5'-3' bias: 2.19

Junction analysis

Reads at junctions: 22,535,627
ACCT 5.53%
AGGT 4.97%
AGGA 3.72%
ATCT 3.59%
TCCT 3.34%
GCCT 2.93%
AGCT 2.76%
AGAT 2.43%
AGGC 2.41%
CCCT 2.29%
TTCT 2.15%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis