Input data and parameters 

Input

Analysis date: Mon Oct 30 22:59:33 GMT 2023
BAM file: SRX7354228.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): 44,902,147 / 44,860,642
Number of aligned pairs (without duplicates): 44,840,145
Total number of alignments: 95,210,306
Number of secondary alignments: 5,447,517
Number of non-unique alignments: 8,989,643
Aligned to genes: 75,360,413
Ambiguous alignments: 257,877
No feature assigned: 10,170,501
Missing chromosome in annotation: 431,872
Not aligned: 690,225

Reads genomic origin

Exonic: 75,360,413 / 88.11%
Intronic: 6,511,971 / 7.61%
Intergenic: 3,658,530 / 4.28%
Intronic/intergenic overlapping exon: 3,640,492 / 4.26%

Transcript coverage profile

5' bias: 0.39
3' bias: 0.23
5'-3' bias: 1.87

Junction analysis

Reads at junctions: 23,212,085
ACCT 5.43%
AGGT 4.63%
TCCT 3.55%
ATCT 3.45%
GCCT 3.38%
AGGA 3.32%
AGCT 2.72%
CCCT 2.53%
AGGC 2.4%
TTCT 2.05%
AGAT 2%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis