Input data and parameters
Input
Analysis date: | Mon Oct 30 12:41:04 GMT 2023 |
BAM file: | SRX7354203.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): | 33,431,998 / 33,410,133 |
Number of aligned pairs (without duplicates): | 33,406,642 |
Total number of alignments: | 70,308,917 |
Number of secondary alignments: | 3,466,786 |
Number of non-unique alignments: | 5,959,437 |
Aligned to genes: | 56,532,785 |
Ambiguous alignments: | 171,928 |
No feature assigned: | 7,476,069 |
Missing chromosome in annotation: | 168,698 |
Not aligned: | 6,873,351 |
Reads genomic origin
Exonic: | 56,532,785 / 88.32% |
Intronic: | 4,207,285 / 6.57% |
Intergenic: | 3,268,784 / 5.11% |
Intronic/intergenic overlapping exon: | 2,249,552 / 3.51% |
Transcript coverage profile
5' bias: | 0.24 |
3' bias: | 0.12 |
5'-3' bias: | 2.15 |
Junction analysis
Reads at junctions: | 15,522,404 |
ACCT | 5.52% |
AGGT | 4.91% |
AGGA | 3.75% |
ATCT | 3.7% |
TCCT | 3.46% |
GCCT | 3.09% |
AGCT | 2.72% |
AGGC | 2.37% |
AGAT | 2.37% |
CCCT | 2.31% |
TTCT | 2.18% |