Input data and parameters 

Input

Analysis date: Tue Oct 31 10:20:12 GMT 2023
BAM file: SRX7354258.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): 113,813,918 / 113,735,862
Number of aligned pairs (without duplicates): 113,711,237
Total number of alignments: 248,352,025
Number of secondary alignments: 20,802,245
Number of non-unique alignments: 31,490,268
Aligned to genes: 192,093,773
Ambiguous alignments: 753,767
No feature assigned: 21,296,539
Missing chromosome in annotation: 2,717,678
Not aligned: 11,235,276

Reads genomic origin

Exonic: 192,093,773 / 90.02%
Intronic: 12,791,682 / 5.99%
Intergenic: 8,504,857 / 3.99%
Intronic/intergenic overlapping exon: 9,332,208 / 4.37%

Transcript coverage profile

5' bias: 0.18
3' bias: 0.17
5'-3' bias: 2.06

Junction analysis

Reads at junctions: 67,932,498
ACCT 5.22%
TCCT 4.56%
ATCT 4.38%
AGGT 4.35%
AGGA 3.07%
CCCT 2.98%
GCCT 2.36%
AGGC 2.27%
AGCT 2.07%
TTCT 1.94%
AGAA 1.72%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis