BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779389.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 = 7,745,044 number of mapped reads = 5,090,418 (65.72%) number of supplementary alignments = 23,027 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,603,284 number of mapped paired reads (second in pair) = 2,487,134 number of mapped paired reads (both in pair) = 4,912,812 number of mapped paired reads (singletons) = 177,606 number of mapped bases = 402,712,295 bp number of sequenced bases = 402,621,715 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 186,309 duplication rate = 2.98% >>>>>>> Insert size mean insert size = 69,165.812 std insert size = 2,516,495.2728 median insert size = 385 >>>>>>> Mapping quality mean mapping quality = 51.9118 >>>>>>> ACTG content number of A's = 124,179,101 bp (30.84%) number of C's = 74,024,885 bp (18.39%) number of T's = 118,963,670 bp (29.55%) number of G's = 85,370,242 bp (21.2%) number of N's = 83,817 bp (0.02%) GC percentage = 39.59% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 2,673,477 number of insertions = 38,996 mapped reads with insertion percentage = 0.76% number of deletions = 44,348 mapped reads with deletion percentage = 0.86% homopolymer indels = 46.52% >>>>>>> Coverage mean coverageData = 0.1301X std coverageData = 0.6923X There is a 8.5% of reference with a coverageData >= 1X There is a 2.48% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% 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 47840559 0.19193757194289998 1.1361772724873735 chr2 243199373 31487699 0.12947278034306445 0.717903895570203 chr3 198022430 26421441 0.1334265062801219 0.5413650649568036 chr4 191154276 39153329 0.204825807820276 0.6660503065162363 chr5 180915260 25147642 0.13900232628248163 0.5306674065936986 chr6 171115067 15921371 0.09304482228908574 0.5534172076151762 chr7 159138663 51986880 0.3266766166057333 1.452570767788097 chr8 146364022 17881120 0.12216882096885805 0.521631068489314 chr9 141213431 18755365 0.13281573053769935 0.6347048216114121 chr10 135534747 11889635 0.0877238882513279 0.5608459728447701 chr11 135006516 22962937 0.1700876200671677 0.6195470420936552 chr12 133851895 12440754 0.09294417535142106 0.439357686547129 chr13 115169878 14425199 0.12525149154017512 0.5354850338075136 chr14 107349540 10597260 0.09871733032111735 0.4483190747350517 chr15 102531392 9882953 0.09638953307100327 0.44465629635761894 chr16 90354753 5386113 0.059610732376192764 0.4252369451492002 chr17 81195210 3244159 0.039955053998875056 0.3266452530700241 chr18 78077248 9027270 0.11561972573623497 0.8039350556358074 chr19 59128983 2984296 0.05047095093788439 0.4957843791180647 chr20 63025520 8587783 0.13625882023662797 0.5530179306856874 chr21 48129895 6814178 0.14157890849335947 0.58999767838028 chr22 51304566 1633562 0.03184047985124755 0.31193523488464286 chrMT 16571 369 0.022267817271136324 0.1612333984133621 chrX 155270560 5651470 0.03639756306668824 0.29256704999130473 chrY 59373566 2588951 0.043604438379193866 0.29551501897468724