Input data and parameters
Input
Analysis date: | Sun Oct 29 01:20:50 GMT 2023 |
BAM file: | SRX7354105.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): | 50,061,270 / 50,020,465 |
Number of aligned pairs (without duplicates): | 50,012,580 |
Total number of alignments: | 106,422,720 |
Number of secondary alignments: | 6,340,985 |
Number of non-unique alignments: | 10,505,566 |
Aligned to genes: | 84,025,171 |
Ambiguous alignments: | 259,803 |
No feature assigned: | 11,163,723 |
Missing chromosome in annotation: | 468,457 |
Not aligned: | 8,516,585 |
Reads genomic origin
Exonic: | 84,025,171 / 88.27% |
Intronic: | 6,685,446 / 7.02% |
Intergenic: | 4,478,277 / 4.7% |
Intronic/intergenic overlapping exon: | 3,323,879 / 3.49% |
Transcript coverage profile
5' bias: | 0.26 |
3' bias: | 0.12 |
5'-3' bias: | 2.3 |
Junction analysis
Reads at junctions: | 27,747,968 |
ACCT | 5.55% |
AGGT | 4.65% |
ATCT | 3.63% |
AGGA | 3.61% |
TCCT | 3.33% |
GCCT | 3.22% |
AGCT | 2.62% |
AGGC | 2.37% |
CCCT | 2.27% |
AGAT | 2.25% |
TTCT | 2.2% |