Input data and parameters 

Input

Analysis date: Sun Oct 29 13:03:20 GMT 2023
BAM file: SRX7354185.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): 45,349,643 / 45,314,964
Number of aligned pairs (without duplicates): 45,305,278
Total number of alignments: 97,083,497
Number of secondary alignments: 6,418,890
Number of non-unique alignments: 10,426,378
Aligned to genes: 76,248,076
Ambiguous alignments: 285,236
No feature assigned: 9,556,886
Missing chromosome in annotation: 566,921
Not aligned: 4,224,585

Reads genomic origin

Exonic: 76,248,076 / 88.86%
Intronic: 6,508,802 / 7.59%
Intergenic: 3,048,084 / 3.55%
Intronic/intergenic overlapping exon: 3,373,471 / 3.93%

Transcript coverage profile

5' bias: 0.33
3' bias: 0.21
5'-3' bias: 2.04

Junction analysis

Reads at junctions: 25,795,808
ACCT 5.08%
AGGT 4.69%
ATCT 4.19%
TCCT 3.57%
GCCT 3.34%
AGGA 3.32%
AGCT 2.6%
CCCT 2.56%
AGGC 2.34%
TTCT 2.08%
AGAT 1.96%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis