Input data and parameters
Input
Analysis date: | Sun Oct 29 12:46:09 GMT 2023 |
BAM file: | SRX7354077.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): | 77,080,409 / 76,937,265 |
Number of aligned pairs (without duplicates): | 76,926,539 |
Total number of alignments: | 163,471,885 |
Number of secondary alignments: | 9,454,211 |
Number of non-unique alignments: | 14,747,971 |
Aligned to genes: | 127,773,214 |
Ambiguous alignments: | 464,162 |
No feature assigned: | 19,359,488 |
Missing chromosome in annotation: | 1,127,050 |
Not aligned: | 12,614,118 |
Reads genomic origin
Exonic: | 127,773,214 / 86.84% |
Intronic: | 12,508,592 / 8.5% |
Intergenic: | 6,850,896 / 4.66% |
Intronic/intergenic overlapping exon: | 6,118,082 / 4.16% |
Transcript coverage profile
5' bias: | 0.49 |
3' bias: | 0.25 |
5'-3' bias: | 1.87 |
Junction analysis
Reads at junctions: | 53,602,932 |
ACCT | 5.15% |
AGGT | 4.77% |
TCCT | 3.54% |
AGGA | 3.44% |
ATCT | 3.36% |
GCCT | 3.12% |
AGCT | 2.81% |
CCCT | 2.53% |
AGGC | 2.41% |
AGAT | 2.18% |
TTCT | 2.17% |