BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818873.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 = 2,177,745 number of mapped reads = 2,113,395 (97.05%) number of supplementary alignments = 34,549 (1.59%) number of secondary alignments = 0 number of mapped bases = 195,602,603 bp number of sequenced bases = 195,478,191 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 589,539 duplication rate = 24.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3691 >>>>>>> ACTG content number of A's = 55,545,476 bp (28.42%) number of C's = 41,353,913 bp (21.16%) number of T's = 56,358,293 bp (28.83%) number of G's = 42,217,419 bp (21.6%) number of N's = 3,090 bp (0%) GC percentage = 42.75% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,187,587 number of insertions = 25,328 mapped reads with insertion percentage = 1.16% number of deletions = 64,204 mapped reads with deletion percentage = 2.97% homopolymer indels = 40.94% >>>>>>> Coverage mean coverageData = 0.0632X std coverageData = 0.7467X There is a 3.98% of reference with a coverageData >= 1X There is a 1.31% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 18531885 0.07435040653318974 1.1844035319076156 chr2 243199373 14847247 0.06104969275558124 1.1182205562174692 chr3 198022430 11871341 0.05994947643052355 0.3545906804486215 chr4 191154276 9890784 0.05174241563918769 0.43481030729670656 chr5 180915260 8691220 0.048040281400253355 0.3390549456389754 chr6 171115067 9600625 0.05610625159034067 0.3861639071662985 chr7 159138663 17396968 0.10931955611566248 1.4929427064325294 chr8 146364022 17424850 0.11905145651162825 0.6396133196332647 chr9 141213431 7161033 0.050710707538860096 0.5751356335286707 chr10 135534747 9012450 0.06649549432515633 0.9694971419124319 chr11 135006516 8482809 0.0628325895025689 0.43956666322896915 chr12 133851895 7667855 0.057286114626916566 0.34901142535656166 chr13 115169878 6069721 0.05270233072574758 0.3298811635118 chr14 107349540 5788472 0.05392172150900693 0.360844458687109 chr15 102531392 5423337 0.052894405256879766 0.330541879129588 chr16 90354753 4916123 0.05440912444307163 0.814279549246136 chr17 81195210 4888179 0.06020280014055016 0.45704777435879906 chr18 78077248 3793680 0.04858880272009587 0.6607579146056367 chr19 59128983 3432054 0.058043514802207916 1.052359279085815 chr20 63025520 8051600 0.12775142513699211 0.5597694651244143 chr21 48129895 1908603 0.03965524961149406 0.34598406188757364 chr22 51304566 1766126 0.03442434343952934 0.30236347203438246 chrMT 16571 331444 20.00144831331845 12.335767146682759 chrX 155270560 7923824 0.051032365697657046 0.3995244624755816 chrY 59373566 730373 0.012301316043574003 0.9558234864983188