Input data and parameters
Input
Analysis date: | Tue Oct 31 09:52:00 GMT 2023 |
BAM file: | SRX7354330.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): | 44,876,832 / 44,805,443 |
Number of aligned pairs (without duplicates): | 44,797,715 |
Total number of alignments: | 95,887,429 |
Number of secondary alignments: | 6,205,154 |
Number of non-unique alignments: | 9,616,604 |
Aligned to genes: | 73,211,538 |
Ambiguous alignments: | 261,017 |
No feature assigned: | 12,007,032 |
Missing chromosome in annotation: | 791,238 |
Not aligned: | 14,309,273 |
Reads genomic origin
Exonic: | 73,211,538 / 85.91% |
Intronic: | 7,214,591 / 8.47% |
Intergenic: | 4,792,441 / 5.62% |
Intronic/intergenic overlapping exon: | 3,276,302 / 3.84% |
Transcript coverage profile
5' bias: | 0.43 |
3' bias: | 0.29 |
5'-3' bias: | 1.74 |
Junction analysis
Reads at junctions: | 26,028,734 |
ACCT | 5.18% |
AGGT | 4.77% |
TCCT | 3.66% |
ATCT | 3.65% |
AGGA | 3.47% |
GCCT | 3.01% |
AGCT | 2.75% |
CCCT | 2.63% |
AGGC | 2.43% |
TTCT | 2.14% |
AGAT | 2.13% |