Input data and parameters 

Input

Analysis date: Sun Oct 29 13:01:28 GMT 2023
BAM file: SRX7354192.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): 40,015,316 / 39,966,036
Number of aligned pairs (without duplicates): 39,960,365
Total number of alignments: 84,729,036
Number of secondary alignments: 4,747,684
Number of non-unique alignments: 7,949,656
Aligned to genes: 65,714,212
Ambiguous alignments: 205,206
No feature assigned: 10,595,464
Missing chromosome in annotation: 264,498
Not aligned: 9,884,664

Reads genomic origin

Exonic: 65,714,212 / 86.12%
Intronic: 6,650,094 / 8.71%
Intergenic: 3,945,370 / 5.17%
Intronic/intergenic overlapping exon: 2,798,897 / 3.67%

Transcript coverage profile

5' bias: 0.33
3' bias: 0.18
5'-3' bias: 1.85

Junction analysis

Reads at junctions: 21,151,392
ACCT 5.6%
AGGT 4.65%
AGGA 3.51%
ATCT 3.5%
GCCT 3.29%
TCCT 3.26%
AGCT 2.8%
CCCT 2.47%
AGAT 2.41%
AGGC 2.36%
TTCT 2.19%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis