Input data and parameters 

Input

Analysis date: Mon Oct 30 19:44:14 GMT 2023
BAM file: SRX7354225.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): 44,234,746 / 44,210,880
Number of aligned pairs (without duplicates): 44,206,827
Total number of alignments: 93,544,680
Number of secondary alignments: 5,099,054
Number of non-unique alignments: 8,442,016
Aligned to genes: 74,519,159
Ambiguous alignments: 280,473
No feature assigned: 9,917,955
Missing chromosome in annotation: 385,077
Not aligned: 1,869,158

Reads genomic origin

Exonic: 74,519,159 / 88.25%
Intronic: 5,910,718 / 7%
Intergenic: 4,007,237 / 4.75%
Intronic/intergenic overlapping exon: 3,165,349 / 3.75%

Transcript coverage profile

5' bias: 0.4
3' bias: 0.25
5'-3' bias: 1.72

Junction analysis

Reads at junctions: 28,864,540
ACCT 5.41%
AGGT 4.58%
TCCT 3.76%
ATCT 3.65%
GCCT 3.65%
AGGA 3.08%
AGCT 2.56%
CCCT 2.5%
AGGC 2.45%
TTCT 2.24%
TCCC 2.04%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis