BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779215.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 = 6,134,572 number of mapped reads = 5,892,925 (96.06%) number of supplementary alignments = 13,286 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,987,231 number of mapped paired reads (second in pair) = 2,905,694 number of mapped paired reads (both in pair) = 5,802,996 number of mapped paired reads (singletons) = 89,929 number of mapped bases = 468,753,520 bp number of sequenced bases = 468,658,859 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,157 duplication rate = 0.61% >>>>>>> Insert size mean insert size = 57,796.5452 std insert size = 2,277,217.9688 median insert size = 261 >>>>>>> Mapping quality mean mapping quality = 52.9504 >>>>>>> ACTG content number of A's = 143,653,105 bp (30.65%) number of C's = 89,901,458 bp (19.18%) number of T's = 143,518,495 bp (30.62%) number of G's = 91,499,575 bp (19.52%) number of N's = 86,226 bp (0.02%) GC percentage = 38.71% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 2,063,290 number of insertions = 36,134 mapped reads with insertion percentage = 0.61% number of deletions = 45,268 mapped reads with deletion percentage = 0.76% homopolymer indels = 46.81% >>>>>>> Coverage mean coverageData = 0.1514X std coverageData = 0.5049X There is a 12.15% of reference with a coverageData >= 1X There is a 2.17% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% 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 0.02% 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 0.01% 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 0.01% 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 38289821 0.15361976169359273 0.5054192266515564 chr2 243199373 44444569 0.18274952131558334 0.4934231751852941 chr3 198022430 30451851 0.1537798066612959 0.43927141048164176 chr4 191154276 34478787 0.18037151834364407 0.47822995311799815 chr5 180915260 32039311 0.17709568004379508 0.4775473323178184 chr6 171115067 27944430 0.16330782840999034 0.4589542739376132 chr7 159138663 44079394 0.27698733399563624 1.108634037524008 chr8 146364022 29199465 0.1994989246742618 0.5131314550636606 chr9 141213431 19160370 0.13568376509455393 0.4321629518585126 chr10 135534747 11343382 0.08369353432297329 0.4603041928879342 chr11 135006516 19597095 0.14515666043852282 0.4351362824756778 chr12 133851895 18646157 0.139304393113 0.424377073596296 chr13 115169878 16118966 0.13995817552224896 0.42055130446113087 chr14 107349540 15436460 0.1437962379717696 0.4431546720417376 chr15 102531392 11152865 0.1087751251831244 0.3813971154698394 chr16 90354753 7000013 0.0774725486771017 0.3117368459404965 chr17 81195210 7884307 0.09710310497380326 0.3611655762153042 chr18 78077248 12989730 0.1663702337459435 0.46500088620475866 chr19 59128983 4410839 0.07459690284204618 0.33798984752102146 chr20 63025520 8155203 0.12939525132041751 0.4218163331646966 chr21 48129895 5384303 0.11187024197746535 0.39229671936202576 chr22 51304566 1856888 0.03619342574694034 0.21461603611236452 chrMT 16571 240 0.014483133184478908 0.11947121844879441 chrX 155270560 28385415 0.18281260143584205 0.5062516053268582 chrY 59373566 303659 0.005114380362466354 0.09111263054189842