Input data and parameters 

Input

Analysis date: Tue Oct 31 09:20:50 GMT 2023
BAM file: SRX7354295.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): 49,861,222 / 49,840,990
Number of aligned pairs (without duplicates): 49,836,748
Total number of alignments: 107,394,066
Number of secondary alignments: 7,691,854
Number of non-unique alignments: 12,470,032
Aligned to genes: 76,243,711
Ambiguous alignments: 235,128
No feature assigned: 17,668,982
Missing chromosome in annotation: 776,213
Not aligned: 2,796,648

Reads genomic origin

Exonic: 76,243,711 / 81.19%
Intronic: 8,596,107 / 9.15%
Intergenic: 9,072,875 / 9.66%
Intronic/intergenic overlapping exon: 3,213,557 / 3.42%

Transcript coverage profile

5' bias: 0.57
3' bias: 0.28
5'-3' bias: 1.84

Junction analysis

Reads at junctions: 24,698,259
ACCT 5.02%
AGGT 4.64%
TCCT 3.58%
ATCT 3.47%
AGGA 3.44%
GCCT 3.34%
AGCT 2.82%
CCCT 2.69%
AGGC 2.36%
TTCT 2.24%
AGAT 2.12%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis