BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231786.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,188,348 number of mapped reads = 3,313,156 (79.1%) number of supplementary alignments = 33,951 (0.81%) number of secondary alignments = 0 number of mapped bases = 215,194,100 bp number of sequenced bases = 215,094,865 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 523,231 duplication rate = 10.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5955 >>>>>>> ACTG content number of A's = 60,723,369 bp (28.23%) number of C's = 41,468,654 bp (19.28%) number of T's = 63,403,119 bp (29.48%) number of G's = 49,484,726 bp (23.01%) number of N's = 14,997 bp (0.01%) GC percentage = 42.29% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,370,444 number of insertions = 14,209 mapped reads with insertion percentage = 0.42% number of deletions = 58,932 mapped reads with deletion percentage = 1.76% homopolymer indels = 45.77% >>>>>>> Coverage mean coverageData = 0.0695X std coverageData = 7.1861X There is a 3.05% of reference with a coverageData >= 1X There is a 1.57% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 7207572 0.028916967071468198 0.41965543719108617 chr2 243199373 37339747 0.1535355397482871 25.499390115888296 chr3 198022430 32631029 0.164784509512382 0.7582292436479114 chr4 191154276 25114271 0.1313822087872102 0.6766214485501745 chr5 180915260 5803043 0.032076028301869064 0.35521281430677676 chr6 171115067 5111763 0.029873248975790075 0.3573630583477383 chr7 159138663 10561305 0.06636542497532483 1.441273774652087 chr8 146364022 4837853 0.03305356694830373 1.441657249968525 chr9 141213431 3883879 0.02750360905826302 0.5124142910826415 chr10 135534747 6535964 0.04822353045747007 0.4379268885166011 chr11 135006516 12436714 0.09211936111291102 1.6915253722385535 chr12 133851895 2575397 0.019240646536980294 0.35076438213983824 chr13 115169878 2971150 0.025797978183149592 0.3170314036172077 chr14 107349540 10040545 0.09353132766102211 0.6683773424443915 chr15 102531392 11875702 0.11582503434655408 0.6369463185289131 chr16 90354753 2906437 0.032166951969864827 0.34711644149499155 chr17 81195210 12321357 0.15174980149691097 1.0125946158479424 chr18 78077248 1822674 0.023344495953545905 0.6853620772346445 chr19 59128983 3428627 0.057985556761563105 0.4737957850905863 chr20 63025520 8077517 0.12816263951491397 0.7045812120035146 chr21 48129895 3325566 0.06909564211598633 0.5009236200777429 chr22 51304566 1049955 0.0204651375474066 0.27388891057634984 chrMT 16571 232900 14.054673827771408 9.432952791404501 chrX 155270560 2566766 0.01653092511548873 0.45750077594509997 chrY 59373566 536367 0.009033767653436884 0.1800042245255437