Input data and parameters 

Input

Analysis date: Sun Oct 29 01:44:39 GMT 2023
BAM file: SRX7354164.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): 41,627,353 / 41,601,806
Number of aligned pairs (without duplicates): 41,597,357
Total number of alignments: 88,640,387
Number of secondary alignments: 5,411,228
Number of non-unique alignments: 9,007,875
Aligned to genes: 70,031,403
Ambiguous alignments: 239,677
No feature assigned: 8,960,517
Missing chromosome in annotation: 400,915
Not aligned: 3,569,389

Reads genomic origin

Exonic: 70,031,403 / 88.66%
Intronic: 5,784,392 / 7.32%
Intergenic: 3,176,125 / 4.02%
Intronic/intergenic overlapping exon: 2,752,850 / 3.48%

Transcript coverage profile

5' bias: 0.39
3' bias: 0.21
5'-3' bias: 1.91

Junction analysis

Reads at junctions: 21,181,027
ACCT 5.16%
AGGT 4.66%
ATCT 3.62%
TCCT 3.59%
AGGA 3.58%
GCCT 3%
AGCT 2.73%
CCCT 2.41%
AGGC 2.34%
TTCT 2.2%
AGAT 2.18%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis