BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818947.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,525,896 number of mapped reads = 1,277,899 (83.75%) number of supplementary alignments = 18,427 (1.21%) number of secondary alignments = 0 number of mapped bases = 118,259,033 bp number of sequenced bases = 118,189,250 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 404,549 duplication rate = 27.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3536 >>>>>>> ACTG content number of A's = 34,915,908 bp (29.54%) number of C's = 24,050,038 bp (20.35%) number of T's = 33,625,795 bp (28.45%) number of G's = 25,592,033 bp (21.65%) number of N's = 5,476 bp (0%) GC percentage = 42% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 759,741 number of insertions = 14,668 mapped reads with insertion percentage = 1.11% number of deletions = 37,661 mapped reads with deletion percentage = 2.88% homopolymer indels = 43.28% >>>>>>> Coverage mean coverageData = 0.0382X std coverageData = 0.4486X There is a 2.29% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 13785951 0.055309595397156505 0.7298038796674533 chr2 243199373 10586951 0.043531983119051876 0.6931296031448095 chr3 198022430 7946149 0.04012751989761968 0.3021765157714359 chr4 191154276 7811922 0.04086710568797321 0.3385760322299898 chr5 180915260 6085186 0.0336355595431806 0.28107022118447234 chr6 171115067 6375331 0.037257566570686615 0.31261119866569936 chr7 159138663 6038593 0.03794548028847019 0.3754094511759653 chr8 146364022 7743188 0.05290362955453629 0.4075310763317735 chr9 141213431 4423829 0.03132725385023752 0.49702353500430085 chr10 135534747 5703548 0.04208181389824707 0.550125300021262 chr11 135006516 4538620 0.03361778478899492 0.3254163718013266 chr12 133851895 5260754 0.03930279806647489 0.30519006159032247 chr13 115169878 1947100 0.016906330316682285 0.19329619819117913 chr14 107349540 2816959 0.0262409973997094 0.2692502114882986 chr15 102531392 3370055 0.03286851894100882 0.2729590836948237 chr16 90354753 3438640 0.03805710143438719 0.5274394941272713 chr17 81195210 2505089 0.03085266975724307 0.29608178194256235 chr18 78077248 2939976 0.03765470832168675 0.5630673232452139 chr19 59128983 1767286 0.029888658832505202 0.606565942806769 chr20 63025520 2520251 0.0399877859000608 0.31500291762081367 chr21 48129895 1589611 0.03302751855161953 0.29567840201453227 chr22 51304566 1418881 0.027656037476274528 0.2669733849563769 chrMT 16571 299001 18.043630438718242 12.042842913542891 chrX 155270560 6956716 0.04480383145394723 0.37794463021569696 chrY 59373566 389446 0.00655924894253446 0.4124564761526477