Input data and parameters
Input
Analysis date: | Tue Oct 31 09:36:33 GMT 2023 |
BAM file: | SRX7354344.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): | 38,731,464 / 38,697,306 |
Number of aligned pairs (without duplicates): | 38,693,744 |
Total number of alignments: | 82,525,911 |
Number of secondary alignments: | 5,097,141 |
Number of non-unique alignments: | 8,680,446 |
Aligned to genes: | 65,071,975 |
Ambiguous alignments: | 240,079 |
No feature assigned: | 8,244,553 |
Missing chromosome in annotation: | 288,858 |
Not aligned: | 3,129,702 |
Reads genomic origin
Exonic: | 65,071,975 / 88.75% |
Intronic: | 5,229,003 / 7.13% |
Intergenic: | 3,015,550 / 4.11% |
Intronic/intergenic overlapping exon: | 2,409,472 / 3.29% |
Transcript coverage profile
5' bias: | 0.31 |
3' bias: | 0.2 |
5'-3' bias: | 1.85 |
Junction analysis
Reads at junctions: | 19,444,197 |
ACCT | 5.34% |
AGGT | 4.6% |
ATCT | 3.68% |
TCCT | 3.67% |
AGGA | 3.46% |
GCCT | 3.34% |
AGCT | 2.64% |
CCCT | 2.61% |
AGGC | 2.44% |
AGAT | 2.23% |
TTCT | 2.16% |