Input data and parameters 

Input

Analysis date: Sun Oct 29 01:24:09 GMT 2023
BAM file: SRX7354121.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): 34,238,502 / 34,221,072
Number of aligned pairs (without duplicates): 34,217,632
Total number of alignments: 72,718,384
Number of secondary alignments: 4,258,810
Number of non-unique alignments: 6,987,413
Aligned to genes: 57,048,141
Ambiguous alignments: 216,830
No feature assigned: 8,155,912
Missing chromosome in annotation: 310,088
Not aligned: 3,391,698

Reads genomic origin

Exonic: 57,048,141 / 87.49%
Intronic: 6,106,600 / 9.37%
Intergenic: 2,049,312 / 3.14%
Intronic/intergenic overlapping exon: 2,120,627 / 3.25%

Transcript coverage profile

5' bias: 0.35
3' bias: 0.21
5'-3' bias: 1.8

Junction analysis

Reads at junctions: 20,814,667
ACCT 5.47%
AGGT 4.54%
AGGA 3.47%
GCCT 3.47%
ATCT 3.46%
TCCT 3.4%
AGCT 2.78%
AGGC 2.37%
CCCT 2.3%
AGAT 2.28%
TTCT 2.01%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis