Input data and parameters 

Input

Analysis date: Sun Oct 29 01:46:28 GMT 2023
BAM file: SRX7354065.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): 32,712,900 / 32,684,729
Number of aligned pairs (without duplicates): 32,677,521
Total number of alignments: 70,794,072
Number of secondary alignments: 5,396,443
Number of non-unique alignments: 8,255,744
Aligned to genes: 55,185,983
Ambiguous alignments: 226,148
No feature assigned: 6,438,792
Missing chromosome in annotation: 687,405
Not aligned: 5,318,069

Reads genomic origin

Exonic: 55,185,983 / 89.55%
Intronic: 3,242,435 / 5.26%
Intergenic: 3,196,357 / 5.19%
Intronic/intergenic overlapping exon: 2,250,811 / 3.65%

Transcript coverage profile

5' bias: 0.15
3' bias: 0.16
5'-3' bias: 1.95

Junction analysis

Reads at junctions: 18,471,170
ACCT 5.53%
TCCT 5.39%
ATCT 4.95%
AGGT 4.06%
CCCT 3.58%
GCCT 2.93%
AGGA 2.83%
TTCT 2.37%
GTCT 2.14%
AGGC 2.03%
AGCT 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