Input data and parameters 

Input

Analysis date: Sun Oct 29 12:28:25 GMT 2023
BAM file: SRX7354138.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): 43,715,050 / 43,665,052
Number of aligned pairs (without duplicates): 43,646,149
Total number of alignments: 94,560,051
Number of secondary alignments: 7,179,949
Number of non-unique alignments: 11,098,380
Aligned to genes: 71,866,756
Ambiguous alignments: 327,264
No feature assigned: 10,319,834
Missing chromosome in annotation: 947,817
Not aligned: 2,527,784

Reads genomic origin

Exonic: 71,866,756 / 87.44%
Intronic: 7,595,518 / 9.24%
Intergenic: 2,724,316 / 3.31%
Intronic/intergenic overlapping exon: 3,765,337 / 4.58%

Transcript coverage profile

5' bias: 0.48
3' bias: 0.22
5'-3' bias: 1.84

Junction analysis

Reads at junctions: 30,056,330
ACCT 5.3%
AGGT 4.76%
TCCT 3.56%
ATCT 3.56%
AGGA 3.34%
GCCT 3.2%
AGCT 2.78%
CCCT 2.71%
AGGC 2.45%
TTCT 2.06%
AGAT 2.03%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis