Input data and parameters 

Input

Analysis date: Mon Oct 30 20:31:41 GMT 2023
BAM file: SRX7354229.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): 44,844,239 / 44,797,146
Number of aligned pairs (without duplicates): 44,769,178
Total number of alignments: 96,009,021
Number of secondary alignments: 6,367,636
Number of non-unique alignments: 9,800,127
Aligned to genes: 73,782,606
Ambiguous alignments: 305,705
No feature assigned: 11,336,793
Missing chromosome in annotation: 783,790
Not aligned: 1,449,497

Reads genomic origin

Exonic: 73,782,606 / 86.68%
Intronic: 8,322,545 / 9.78%
Intergenic: 3,014,248 / 3.54%
Intronic/intergenic overlapping exon: 3,847,373 / 4.52%

Transcript coverage profile

5' bias: 0.47
3' bias: 0.23
5'-3' bias: 2

Junction analysis

Reads at junctions: 28,163,303
ACCT 5.04%
AGGT 4.7%
ATCT 3.65%
TCCT 3.6%
AGGA 3.43%
GCCT 3.02%
AGCT 2.77%
CCCT 2.66%
AGGC 2.39%
AGAT 2.06%
TTCT 2.06%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis