Input data and parameters
Input
Analysis date: | Sun Oct 29 12:31:41 GMT 2023 |
BAM file: | SRX7354053.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): | 51,044,898 / 50,992,946 |
Number of aligned pairs (without duplicates): | 50,983,671 |
Total number of alignments: | 108,609,243 |
Number of secondary alignments: | 6,571,399 |
Number of non-unique alignments: | 10,895,139 |
Aligned to genes: | 83,032,237 |
Ambiguous alignments: | 311,458 |
No feature assigned: | 13,934,617 |
Missing chromosome in annotation: | 435,792 |
Not aligned: | 11,688,798 |
Reads genomic origin
Exonic: | 83,032,237 / 85.63% |
Intronic: | 9,417,872 / 9.71% |
Intergenic: | 4,516,745 / 4.66% |
Intronic/intergenic overlapping exon: | 3,492,583 / 3.6% |
Transcript coverage profile
5' bias: | 0.34 |
3' bias: | 0.19 |
5'-3' bias: | 1.94 |
Junction analysis
Reads at junctions: | 25,645,879 |
ACCT | 5.32% |
AGGT | 4.78% |
AGGA | 3.58% |
TCCT | 3.56% |
ATCT | 3.53% |
GCCT | 2.95% |
AGCT | 2.65% |
CCCT | 2.4% |
AGGC | 2.38% |
AGAT | 2.31% |
TTCT | 2.31% |