Input data and parameters 

Input

Analysis date: Tue Oct 31 18:04:17 GMT 2023
BAM file: SRX7354347.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): 52,167,326 / 52,125,885
Number of aligned pairs (without duplicates): 52,113,449
Total number of alignments: 134,902,063
Number of secondary alignments: 30,608,852
Number of non-unique alignments: 25,019,849
Aligned to genes: 83,252,552
Ambiguous alignments: 381,211
No feature assigned: 11,848,255
Missing chromosome in annotation: 14,400,196
Not aligned: 6,522,903

Reads genomic origin

Exonic: 83,252,552 / 87.54%
Intronic: 7,746,584 / 8.15%
Intergenic: 4,101,671 / 4.31%
Intronic/intergenic overlapping exon: 3,642,252 / 3.83%

Transcript coverage profile

5' bias: 0.23
3' bias: 0.21
5'-3' bias: 2

Junction analysis

Reads at junctions: 28,971,195
ACCT 5.45%
AGGT 4.47%
TCCT 4.41%
ATCT 4.15%
CCCT 3.25%
GCCT 3.21%
AGGA 3.01%
AGGC 2.38%
AGCT 2.21%
TTCT 2.15%
AGAA 1.74%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis