Input data and parameters 

Input

Analysis date: Tue Oct 31 15:47:32 GMT 2023
BAM file: SRX7354413.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): 37,672,066 / 37,645,130
Number of aligned pairs (without duplicates): 37,639,967
Total number of alignments: 81,221,889
Number of secondary alignments: 5,904,693
Number of non-unique alignments: 9,958,286
Aligned to genes: 64,597,511
Ambiguous alignments: 252,937
No feature assigned: 5,993,999
Missing chromosome in annotation: 419,156
Not aligned: 2,696,946

Reads genomic origin

Exonic: 64,597,511 / 91.51%
Intronic: 3,258,735 / 4.62%
Intergenic: 2,735,264 / 3.87%
Intronic/intergenic overlapping exon: 2,419,799 / 3.43%

Transcript coverage profile

5' bias: 0.18
3' bias: 0.2
5'-3' bias: 1.8

Junction analysis

Reads at junctions: 19,443,398
ACCT 5.58%
TCCT 4.75%
ATCT 4.56%
AGGT 4.38%
GCCT 3.36%
AGGA 2.96%
CCCT 2.93%
TTCT 2.27%
AGGC 2.23%
AGCT 2.18%
TCCC 2.13%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis