Input data and parameters
Input
Analysis date: | Mon Oct 30 22:50:23 GMT 2023 |
BAM file: | SRX7354216.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): | 51,764,901 / 51,736,782 |
Number of aligned pairs (without duplicates): | 51,731,811 |
Total number of alignments: | 109,966,485 |
Number of secondary alignments: | 6,464,802 |
Number of non-unique alignments: | 10,731,538 |
Aligned to genes: | 85,062,383 |
Ambiguous alignments: | 252,777 |
No feature assigned: | 13,403,655 |
Missing chromosome in annotation: | 516,132 |
Not aligned: | 5,357,543 |
Reads genomic origin
Exonic: | 85,062,383 / 86.39% |
Intronic: | 8,339,899 / 8.47% |
Intergenic: | 5,063,756 / 5.14% |
Intronic/intergenic overlapping exon: | 3,572,316 / 3.63% |
Transcript coverage profile
5' bias: | 0.36 |
3' bias: | 0.2 |
5'-3' bias: | 1.99 |
Junction analysis
Reads at junctions: | 23,881,708 |
ACCT | 5.38% |
AGGT | 4.78% |
AGGA | 3.65% |
ATCT | 3.51% |
TCCT | 3.47% |
GCCT | 2.98% |
AGCT | 2.72% |
CCCT | 2.39% |
AGGC | 2.39% |
AGAT | 2.35% |
TTCT | 2.12% |