Input data and parameters
Input
Analysis date: | Tue Oct 31 18:08:09 GMT 2023 |
BAM file: | SRX7354403.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): | 53,575,022 / 53,530,134 |
Number of aligned pairs (without duplicates): | 53,521,751 |
Total number of alignments: | 113,705,171 |
Number of secondary alignments: | 6,600,015 |
Number of non-unique alignments: | 11,095,750 |
Aligned to genes: | 88,668,174 |
Ambiguous alignments: | 284,189 |
No feature assigned: | 13,266,174 |
Missing chromosome in annotation: | 390,884 |
Not aligned: | 9,399,940 |
Reads genomic origin
Exonic: | 88,668,174 / 86.99% |
Intronic: | 8,399,372 / 8.24% |
Intergenic: | 4,866,802 / 4.77% |
Intronic/intergenic overlapping exon: | 3,678,841 / 3.61% |
Transcript coverage profile
5' bias: | 0.34 |
3' bias: | 0.19 |
5'-3' bias: | 1.96 |
Junction analysis
Reads at junctions: | 28,778,570 |
ACCT | 5.38% |
AGGT | 4.64% |
ATCT | 3.75% |
TCCT | 3.6% |
AGGA | 3.47% |
GCCT | 3.25% |
AGCT | 2.66% |
AGGC | 2.46% |
CCCT | 2.41% |
AGAT | 2.25% |
TTCT | 2.23% |