Input data and parameters 

Input

Analysis date: Sun Oct 29 12:35:43 GMT 2023
BAM file: SRX7354140.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): 103,680,630 / 103,557,076
Number of aligned pairs (without duplicates): 103,538,379
Total number of alignments: 221,428,415
Number of secondary alignments: 14,190,709
Number of non-unique alignments: 23,931,912
Aligned to genes: 171,102,614
Ambiguous alignments: 650,177
No feature assigned: 24,801,147
Missing chromosome in annotation: 942,565
Not aligned: 6,840,020

Reads genomic origin

Exonic: 171,102,614 / 87.34%
Intronic: 16,858,786 / 8.61%
Intergenic: 7,942,361 / 4.05%
Intronic/intergenic overlapping exon: 7,689,064 / 3.92%

Transcript coverage profile

5' bias: 0.45
3' bias: 0.22
5'-3' bias: 1.81

Junction analysis

Reads at junctions: 56,212,798
ACCT 5.17%
AGGT 4.88%
AGGA 3.6%
TCCT 3.47%
ATCT 3.43%
GCCT 3.01%
AGCT 2.76%
CCCT 2.62%
AGGC 2.54%
AGAT 2.32%
TTCT 2.23%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis