BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081213.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,028,927 number of mapped reads = 1,783,452 (87.9%) number of supplementary alignments = 21,110 (1.04%) number of secondary alignments = 0 number of mapped bases = 116,066,911 bp number of sequenced bases = 116,023,214 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,442 duplication rate = 3.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.127 >>>>>>> ACTG content number of A's = 32,852,258 bp (28.32%) number of C's = 22,410,828 bp (19.32%) number of T's = 35,525,424 bp (30.62%) number of G's = 25,219,234 bp (21.74%) number of N's = 15,470 bp (0.01%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,053,835 number of insertions = 8,970 mapped reads with insertion percentage = 0.5% number of deletions = 26,665 mapped reads with deletion percentage = 1.48% homopolymer indels = 48.14% >>>>>>> Coverage mean coverageData = 0.0375X std coverageData = 0.2892X There is a 3.14% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% 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 11415884 0.04580082470486603 0.41753073013009634 chr2 243199373 7341758 0.030188227500076655 0.34405405462404004 chr3 198022430 6749397 0.034084002504160764 0.21307400529975726 chr4 191154276 3964252 0.020738495015408392 0.17638710127087473 chr5 180915260 7464748 0.04126101910916746 0.2352066143270222 chr6 171115067 7219976 0.04219368946628178 0.2522385488511366 chr7 159138663 7503364 0.047149849436651355 0.4156800469517231 chr8 146364022 6480603 0.04427729514019504 0.34047548124591864 chr9 141213431 3378479 0.023924629378915097 0.23171468745247217 chr10 135534747 4125816 0.030441020412278485 0.2699835723632266 chr11 135006516 6035893 0.04470816060463333 0.31688220783555876 chr12 133851895 3153755 0.023561526715777912 0.17900153401589192 chr13 115169878 4146925 0.03600702780982368 0.22032151238990952 chr14 107349540 5057852 0.04711573053782997 0.254572111294889 chr15 102531392 4695478 0.04579551597231802 0.2538023251184595 chr16 90354753 4181007 0.04627323811067249 0.25990784516425913 chr17 81195210 2116184 0.026062916765656495 0.20111490161179615 chr18 78077248 4055088 0.0519368715454725 0.3973054399037064 chr19 59128983 3254849 0.055046591956435305 0.3760471007328521 chr20 63025520 2794160 0.0443337873293231 0.24572705808805617 chr21 48129895 1804356 0.03748929849109374 0.23316031308913127 chr22 51304566 905083 0.017641373284397337 0.1502290498729548 chrMT 16571 100300 6.052742743346811 4.807340586274112 chrX 155270560 7800875 0.05024052853290411 0.2787297592254415 chrY 59373566 320829 0.005403566294131634 0.11532228225021025