Input data and parameters 

Input

Analysis date: Sun Oct 29 01:37:09 GMT 2023
BAM file: SRX7354114.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): 66,094,328 / 66,036,400
Number of aligned pairs (without duplicates): 66,030,416
Total number of alignments: 140,408,542
Number of secondary alignments: 8,277,814
Number of non-unique alignments: 12,731,072
Aligned to genes: 105,866,826
Ambiguous alignments: 417,785
No feature assigned: 20,327,486
Missing chromosome in annotation: 1,065,373
Not aligned: 6,184,588

Reads genomic origin

Exonic: 105,866,826 / 83.89%
Intronic: 13,218,117 / 10.47%
Intergenic: 7,109,369 / 5.63%
Intronic/intergenic overlapping exon: 4,960,922 / 3.93%

Transcript coverage profile

5' bias: 0.44
3' bias: 0.29
5'-3' bias: 1.66

Junction analysis

Reads at junctions: 42,584,929
ACCT 5.18%
AGGT 4.71%
GCCT 3.7%
TCCT 3.51%
ATCT 3.49%
AGGA 3.38%
AGCT 2.81%
CCCT 2.77%
AGGC 2.51%
TTCT 2.21%
AGAT 2.13%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis