Input data and parameters 

Input

Analysis date: Sun Oct 29 01:26:24 GMT 2023
BAM file: SRX7354068.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): 33,952,192 / 33,925,553
Number of aligned pairs (without duplicates): 33,899,710
Total number of alignments: 74,218,029
Number of secondary alignments: 6,340,284
Number of non-unique alignments: 9,194,316
Aligned to genes: 56,055,718
Ambiguous alignments: 234,839
No feature assigned: 7,697,664
Missing chromosome in annotation: 1,035,492
Not aligned: 2,449,813

Reads genomic origin

Exonic: 56,055,718 / 87.93%
Intronic: 5,411,006 / 8.49%
Intergenic: 2,286,658 / 3.59%
Intronic/intergenic overlapping exon: 3,396,109 / 5.33%

Transcript coverage profile

5' bias: 0.24
3' bias: 0.2
5'-3' bias: 1.99

Junction analysis

Reads at junctions: 20,882,564
ACCT 5.28%
TCCT 4.48%
AGGT 4.44%
ATCT 4.24%
AGGA 3.08%
GCCT 3%
CCCT 2.96%
AGGC 2.39%
AGCT 2.27%
TTCT 2.05%
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