Input data and parameters 

Input

Analysis date: Tue Oct 31 17:17:40 GMT 2023
BAM file: SRX7354401.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): 35,161,702 / 35,125,875
Number of aligned pairs (without duplicates): 35,122,511
Total number of alignments: 74,719,937
Number of secondary alignments: 4,432,360
Number of non-unique alignments: 7,374,221
Aligned to genes: 59,352,161
Ambiguous alignments: 221,891
No feature assigned: 7,467,863
Missing chromosome in annotation: 303,801
Not aligned: 6,827,319

Reads genomic origin

Exonic: 59,352,161 / 88.82%
Intronic: 4,979,920 / 7.45%
Intergenic: 2,487,943 / 3.72%
Intronic/intergenic overlapping exon: 2,107,115 / 3.15%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.22
5'-3' bias: 1.93

Junction analysis

Reads at junctions: 19,942,023
ACCT 5.25%
AGGT 4.76%
ATCT 3.66%
AGGA 3.54%
TCCT 3.43%
GCCT 3.11%
AGCT 2.74%
TTCT 2.37%
AGGC 2.36%
CCCT 2.36%
AGAT 2.23%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis