Input data and parameters 

Input

Analysis date: Sun Oct 29 01:43:00 GMT 2023
BAM file: SRX7354153.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): 59,193,792 / 59,148,949
Number of aligned pairs (without duplicates): 59,143,194
Total number of alignments: 125,818,125
Number of secondary alignments: 7,475,384
Number of non-unique alignments: 12,439,347
Aligned to genes: 97,808,259
Ambiguous alignments: 327,551
No feature assigned: 14,719,792
Missing chromosome in annotation: 523,176
Not aligned: 4,212,999

Reads genomic origin

Exonic: 97,808,259 / 86.92%
Intronic: 9,256,216 / 8.23%
Intergenic: 5,463,576 / 4.86%
Intronic/intergenic overlapping exon: 4,035,873 / 3.59%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.18
5'-3' bias: 1.87

Junction analysis

Reads at junctions: 29,515,488
ACCT 5.48%
AGGT 4.65%
AGGA 3.52%
ATCT 3.46%
GCCT 3.43%
TCCT 3.28%
AGCT 2.69%
CCCT 2.43%
AGGC 2.42%
TTCT 2.29%
AGAT 2.25%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis