Input data and parameters 

Input

Analysis date: Tue Oct 31 09:44:32 GMT 2023
BAM file: SRX7354343.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): 46,486,442 / 46,468,917
Number of aligned pairs (without duplicates): 46,461,217
Total number of alignments: 118,332,330
Number of secondary alignments: 25,376,971
Number of non-unique alignments: 23,237,134
Aligned to genes: 74,638,325
Ambiguous alignments: 312,368
No feature assigned: 9,357,783
Missing chromosome in annotation: 10,786,720
Not aligned: 2,593,917

Reads genomic origin

Exonic: 74,638,325 / 88.86%
Intronic: 6,075,923 / 7.23%
Intergenic: 3,281,860 / 3.91%
Intronic/intergenic overlapping exon: 3,113,143 / 3.71%

Transcript coverage profile

5' bias: 0.2
3' bias: 0.21
5'-3' bias: 1.71

Junction analysis

Reads at junctions: 23,088,997
ACCT 5.23%
AGGT 4.48%
ATCT 4.29%
TCCT 4.26%
CCCT 3.25%
GCCT 3.18%
AGGA 3.05%
AGGC 2.32%
AGCT 2.17%
TTCT 2.17%
GTCT 1.76%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis