BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779393.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 16,113,970 number of mapped reads = 14,403,765 (89.39%) number of supplementary alignments = 128,666 (0.8%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,245,962 number of mapped paired reads (second in pair) = 7,157,803 number of mapped paired reads (both in pair) = 14,243,074 number of mapped paired reads (singletons) = 160,691 number of mapped bases = 1,141,814,020 bp number of sequenced bases = 1,141,541,458 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,939,895 duplication rate = 12.94% >>>>>>> Insert size mean insert size = 113,081.5571 std insert size = 3,127,345.5536 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 52.6313 >>>>>>> ACTG content number of A's = 351,692,413 bp (30.81%) number of C's = 218,545,951 bp (19.14%) number of T's = 346,008,195 bp (30.31%) number of G's = 225,039,828 bp (19.71%) number of N's = 255,071 bp (0.02%) GC percentage = 38.86% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 4,594,514 number of insertions = 114,465 mapped reads with insertion percentage = 0.79% number of deletions = 137,792 mapped reads with deletion percentage = 0.94% homopolymer indels = 46.5% >>>>>>> Coverage mean coverageData = 0.3688X std coverageData = 16.2489X There is a 6.45% of reference with a coverageData >= 1X There is a 3.48% of reference with a coverageData >= 2X There is a 2.35% of reference with a coverageData >= 3X There is a 1.76% of reference with a coverageData >= 4X There is a 1.39% of reference with a coverageData >= 5X There is a 1.14% of reference with a coverageData >= 6X There is a 0.95% of reference with a coverageData >= 7X There is a 0.81% of reference with a coverageData >= 8X There is a 0.7% of reference with a coverageData >= 9X There is a 0.62% of reference with a coverageData >= 10X There is a 0.54% of reference with a coverageData >= 11X There is a 0.48% of reference with a coverageData >= 12X There is a 0.43% of reference with a coverageData >= 13X There is a 0.39% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.18% of reference with a coverageData >= 23X There is a 0.17% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.14% of reference with a coverageData >= 27X There is a 0.13% of reference with a coverageData >= 28X There is a 0.12% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.08% of reference with a coverageData >= 37X There is a 0.08% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.07% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 74903112 0.3005132412488553 16.66930013552256 chr2 243199373 83749536 0.34436575623901794 8.175069739628665 chr3 198022430 85157888 0.4300416271025459 15.861594212785224 chr4 191154276 106235314 0.5557569321650958 16.298762171120703 chr5 180915260 80114151 0.4428269400823347 12.66775506477461 chr6 171115067 79476605 0.4644629277444049 11.787906473549164 chr7 159138663 62626029 0.3935311998945222 7.189255031449577 chr8 146364022 61281354 0.4186913775845815 12.060872776708505 chr9 141213431 38278077 0.2710654130342602 6.679227451779483 chr10 135534747 48759791 0.35975860123898706 12.654883808346229 chr11 135006516 36771652 0.2723694610414211 6.090208943032642 chr12 133851895 59228169 0.4424903285829461 16.5867993731249 chr13 115169878 45174825 0.3922451406955558 19.899002638272673 chr14 107349540 35448106 0.33021199718228883 7.495799405001759 chr15 102531392 21422555 0.20893654696505046 7.764712102237761 chr16 90354753 29658185 0.3282415591352455 10.804097081454106 chr17 81195210 25285960 0.3114218190949934 35.42469908508299 chr18 78077248 51346406 0.6576359607346817 32.395730849559946 chr19 59128983 11761374 0.19891047339677734 7.000705371632574 chr20 63025520 12717875 0.20178929106812604 4.873705053463932 chr21 48129895 13809335 0.286918037116017 3.999657745153818 chr22 51304566 30712374 0.598628472951121 65.04509269449517 chrMT 16571 11376 0.6865005129443003 1.0192608074268392 chrX 155270560 41528830 0.26746106924583773 5.325172689003894 chrY 59373566 6355141 0.10703653878562726 1.8476872150216617