Input data and parameters
Input
Analysis date: | Mon Oct 30 20:18:28 GMT 2023 |
BAM file: | SRX7354248.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): | 43,952,706 / 43,935,119 |
Number of aligned pairs (without duplicates): | 43,910,265 |
Total number of alignments: | 95,208,361 |
Number of secondary alignments: | 7,320,536 |
Number of non-unique alignments: | 11,875,802 |
Aligned to genes: | 74,847,809 |
Ambiguous alignments: | 278,911 |
No feature assigned: | 7,544,234 |
Missing chromosome in annotation: | 661,605 |
Not aligned: | 3,592,109 |
Reads genomic origin
Exonic: | 74,847,809 / 90.84% |
Intronic: | 4,301,060 / 5.22% |
Intergenic: | 3,243,174 / 3.94% |
Intronic/intergenic overlapping exon: | 3,308,996 / 4.02% |
Transcript coverage profile
5' bias: | 0.1 |
3' bias: | 0.15 |
5'-3' bias: | 1.54 |
Junction analysis
Reads at junctions: | 24,602,331 |
ACCT | 4.85% |
ATCT | 4.82% |
TCCT | 4.6% |
AGGT | 4.41% |
CCCT | 3.5% |
AGGA | 2.84% |
AGGC | 2.5% |
GCCT | 2.26% |
AGAC | 2.14% |
TTCT | 2.03% |
AGCT | 2.01% |