BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779390.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 = 9,160,078 number of mapped reads = 6,955,698 (75.93%) number of supplementary alignments = 35,764 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,519,841 number of mapped paired reads (second in pair) = 3,435,857 number of mapped paired reads (both in pair) = 6,818,070 number of mapped paired reads (singletons) = 137,628 number of mapped bases = 551,112,636 bp number of sequenced bases = 550,988,027 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 271,696 duplication rate = 3.36% >>>>>>> Insert size mean insert size = 48,853.452 std insert size = 2,074,293.3109 median insert size = 334 >>>>>>> Mapping quality mean mapping quality = 52.761 >>>>>>> ACTG content number of A's = 171,982,287 bp (31.21%) number of C's = 99,545,767 bp (18.07%) number of T's = 163,508,583 bp (29.68%) number of G's = 115,835,958 bp (21.02%) number of N's = 115,432 bp (0.02%) GC percentage = 39.09% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 3,563,943 number of insertions = 52,744 mapped reads with insertion percentage = 0.75% number of deletions = 60,451 mapped reads with deletion percentage = 0.86% homopolymer indels = 46.94% >>>>>>> Coverage mean coverageData = 0.178X std coverageData = 0.81X There is a 11.12% of reference with a coverageData >= 1X There is a 3.56% of reference with a coverageData >= 2X There is a 1.43% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 40575423 0.16278965660029387 1.2461658974347944 chr2 243199373 49035650 0.20162737014951104 0.8361605935654827 chr3 198022430 40256446 0.20329235430551984 0.6860612495387627 chr4 191154276 43104007 0.22549329213017447 0.8030557998128369 chr5 180915260 57966817 0.32040866536078827 0.8660209070933312 chr6 171115067 24795276 0.14490410712926874 0.6090595158927449 chr7 159138663 54559580 0.342843021120518 1.144593392842797 chr8 146364022 28127757 0.1921767153952629 0.6735370785004583 chr9 141213431 20135829 0.14259145789043254 0.6430877597600833 chr10 135534747 13234593 0.09764723285313691 1.143787668858039 chr11 135006516 26412752 0.1956405718965446 0.6811086713871458 chr12 133851895 23781649 0.177671365803226 0.6380789852374107 chr13 115169878 20374721 0.17691015527514928 0.7869471813814878 chr14 107349540 13691153 0.1275380686307552 0.560013080298633 chr15 102531392 12825733 0.12509079170601722 0.5580994661082442 chr16 90354753 11609244 0.12848515008391423 0.5741180145220226 chr17 81195210 9857628 0.12140652139455024 0.5691697929066477 chr18 78077248 17206525 0.22037822081024167 0.8643556221966942 chr19 59128983 5328045 0.09010885575353123 1.1260723661283718 chr20 63025520 9067320 0.14386743655585865 0.5633354126594199 chr21 48129895 6339518 0.1317168466708685 0.5559383274884914 chr22 51304566 2922971 0.05697292127956018 0.407077011754761 chrMT 16571 3186 0.1922635930239575 0.5130279193629167 chrX 155270560 17235160 0.11100082333701894 0.5043925766670726 chrY 59373566 2665653 0.04489629273741112 0.3492617352405387