Input data and parameters 

Input

Analysis date: Mon Oct 30 22:50:23 GMT 2023
BAM file: SRX7354216.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): 51,764,901 / 51,736,782
Number of aligned pairs (without duplicates): 51,731,811
Total number of alignments: 109,966,485
Number of secondary alignments: 6,464,802
Number of non-unique alignments: 10,731,538
Aligned to genes: 85,062,383
Ambiguous alignments: 252,777
No feature assigned: 13,403,655
Missing chromosome in annotation: 516,132
Not aligned: 5,357,543

Reads genomic origin

Exonic: 85,062,383 / 86.39%
Intronic: 8,339,899 / 8.47%
Intergenic: 5,063,756 / 5.14%
Intronic/intergenic overlapping exon: 3,572,316 / 3.63%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.2
5'-3' bias: 1.99

Junction analysis

Reads at junctions: 23,881,708
ACCT 5.38%
AGGT 4.78%
AGGA 3.65%
ATCT 3.51%
TCCT 3.47%
GCCT 2.98%
AGCT 2.72%
CCCT 2.39%
AGGC 2.39%
AGAT 2.35%
TTCT 2.12%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis