Input data and parameters 

Input

Analysis date: Sun Oct 29 01:07:09 GMT 2023
BAM file: SRX7354144.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): 32,687,334 / 32,659,377
Number of aligned pairs (without duplicates): 32,655,055
Total number of alignments: 69,605,442
Number of secondary alignments: 4,258,731
Number of non-unique alignments: 7,112,599
Aligned to genes: 53,017,987
Ambiguous alignments: 186,025
No feature assigned: 9,034,700
Missing chromosome in annotation: 254,131
Not aligned: 5,777,527

Reads genomic origin

Exonic: 53,017,987 / 85.44%
Intronic: 6,192,600 / 9.98%
Intergenic: 2,842,100 / 4.58%
Intronic/intergenic overlapping exon: 2,276,300 / 3.67%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.18
5'-3' bias: 1.88

Junction analysis

Reads at junctions: 17,942,087
ACCT 5.54%
AGGT 4.78%
AGGA 3.64%
ATCT 3.58%
TCCT 3.38%
GCCT 3.18%
AGCT 2.71%
AGAT 2.44%
CCCT 2.43%
AGGC 2.38%
TTCT 2.17%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis