Input data and parameters
Input
Analysis date: | Sun Oct 29 11:50:32 GMT 2023 |
BAM file: | SRX7354082.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): | 43,552,404 / 43,527,084 |
Number of aligned pairs (without duplicates): | 43,519,417 |
Total number of alignments: | 94,720,534 |
Number of secondary alignments: | 7,641,046 |
Number of non-unique alignments: | 10,881,474 |
Aligned to genes: | 73,211,439 |
Ambiguous alignments: | 290,581 |
No feature assigned: | 8,947,647 |
Missing chromosome in annotation: | 1,389,393 |
Not aligned: | 2,262,624 |
Reads genomic origin
Exonic: | 73,211,439 / 89.11% |
Intronic: | 5,979,141 / 7.28% |
Intergenic: | 2,968,506 / 3.61% |
Intronic/intergenic overlapping exon: | 3,178,387 / 3.87% |
Transcript coverage profile
5' bias: | 0.28 |
3' bias: | 0.23 |
5'-3' bias: | 1.71 |
Junction analysis
Reads at junctions: | 25,129,896 |
ACCT | 5.34% |
AGGT | 4.27% |
ATCT | 4.21% |
TCCT | 4.17% |
GCCT | 3.55% |
AGGA | 3.06% |
CCCT | 2.59% |
AGCT | 2.44% |
AGGC | 2.31% |
TTCT | 2.19% |
TCCC | 1.9% |