Input data and parameters 

Input

Analysis date: Mon Oct 30 20:21:35 GMT 2023
BAM file: SRX7354231.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): 38,119,584 / 38,089,682
Number of aligned pairs (without duplicates): 38,086,376
Total number of alignments: 81,282,086
Number of secondary alignments: 5,072,820
Number of non-unique alignments: 8,301,638
Aligned to genes: 63,716,105
Ambiguous alignments: 237,206
No feature assigned: 8,683,383
Missing chromosome in annotation: 343,754
Not aligned: 5,145,444

Reads genomic origin

Exonic: 63,716,105 / 88.01%
Intronic: 5,893,560 / 8.14%
Intergenic: 2,789,823 / 3.85%
Intronic/intergenic overlapping exon: 2,295,159 / 3.17%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.18
5'-3' bias: 2

Junction analysis

Reads at junctions: 23,099,454
ACCT 5.66%
AGGT 4.83%
AGGA 3.77%
TCCT 3.46%
ATCT 3.43%
GCCT 2.89%
AGCT 2.82%
AGGC 2.46%
AGAT 2.44%
CCCT 2.38%
TTCT 2.24%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis