Input data and parameters 

Input

Analysis date: Mon Oct 30 20:44:42 GMT 2023
BAM file: SRX7354246.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): 43,248,477 / 43,222,205
Number of aligned pairs (without duplicates): 43,208,977
Total number of alignments: 93,399,191
Number of secondary alignments: 6,928,509
Number of non-unique alignments: 11,487,446
Aligned to genes: 73,091,054
Ambiguous alignments: 271,737
No feature assigned: 7,993,070
Missing chromosome in annotation: 555,884
Not aligned: 5,187,670

Reads genomic origin

Exonic: 73,091,054 / 90.14%
Intronic: 5,307,546 / 6.55%
Intergenic: 2,685,524 / 3.31%
Intronic/intergenic overlapping exon: 3,570,643 / 4.4%

Transcript coverage profile

5' bias: 0.24
3' bias: 0.16
5'-3' bias: 2.28

Junction analysis

Reads at junctions: 23,805,056
ACCT 5.14%
AGGT 4.81%
ATCT 4.22%
TCCT 3.88%
AGGA 3.31%
GCCT 2.97%
CCCT 2.76%
AGCT 2.38%
AGGC 2.31%
TTCT 2.14%
AGAA 2%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis