Input data and parameters 

Input

Analysis date: Tue Oct 31 09:42:07 GMT 2023
BAM file: SRX7354260.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): 51,903,999 / 51,867,385
Number of aligned pairs (without duplicates): 51,855,078
Total number of alignments: 109,821,579
Number of secondary alignments: 6,050,195
Number of non-unique alignments: 10,073,428
Aligned to genes: 85,488,259
Ambiguous alignments: 262,474
No feature assigned: 13,528,892
Missing chromosome in annotation: 468,526
Not aligned: 5,658,446

Reads genomic origin

Exonic: 85,488,259 / 86.34%
Intronic: 9,367,011 / 9.46%
Intergenic: 4,161,881 / 4.2%
Intronic/intergenic overlapping exon: 4,194,168 / 4.24%

Transcript coverage profile

5' bias: 0.3
3' bias: 0.16
5'-3' bias: 1.87

Junction analysis

Reads at junctions: 27,726,423
ACCT 5.55%
AGGT 4.67%
ATCT 3.55%
AGGA 3.53%
GCCT 3.25%
TCCT 3.21%
AGCT 2.78%
AGAT 2.39%
AGGC 2.39%
CCCT 2.29%
TTCT 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