Input data and parameters
Input
Analysis date: | Sun Oct 29 01:45:13 GMT 2023 |
BAM file: | SRX7354100.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): | 42,907,737 / 42,873,796 |
Number of aligned pairs (without duplicates): | 42,864,362 |
Total number of alignments: | 92,994,472 |
Number of secondary alignments: | 7,212,939 |
Number of non-unique alignments: | 11,525,659 |
Aligned to genes: | 73,128,212 |
Ambiguous alignments: | 262,473 |
No feature assigned: | 7,325,431 |
Missing chromosome in annotation: | 752,697 |
Not aligned: | 3,021,345 |
Reads genomic origin
Exonic: | 73,128,212 / 90.89% |
Intronic: | 4,641,559 / 5.77% |
Intergenic: | 2,683,872 / 3.34% |
Intronic/intergenic overlapping exon: | 2,656,827 / 3.3% |
Transcript coverage profile
5' bias: | 0.34 |
3' bias: | 0.23 |
5'-3' bias: | 1.79 |
Junction analysis
Reads at junctions: | 22,030,480 |
AGGT | 5.03% |
ACCT | 5.02% |
AGGA | 3.6% |
TCCT | 3.6% |
ATCT | 3.52% |
GCCT | 2.68% |
AGCT | 2.62% |
AGGC | 2.47% |
CCCT | 2.44% |
AGAT | 2.1% |
TTCT | 2.02% |