BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084871.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 = 2,736,781 number of mapped reads = 2,493,789 (91.12%) number of supplementary alignments = 18,945 (0.69%) number of secondary alignments = 0 number of mapped bases = 173,330,976 bp number of sequenced bases = 173,263,528 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,363 duplication rate = 4.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9716 >>>>>>> ACTG content number of A's = 50,732,160 bp (29.28%) number of C's = 31,571,781 bp (18.22%) number of T's = 55,835,270 bp (32.23%) number of G's = 35,097,285 bp (20.26%) number of N's = 27,032 bp (0.02%) GC percentage = 38.48% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,428,431 number of insertions = 13,963 mapped reads with insertion percentage = 0.56% number of deletions = 38,255 mapped reads with deletion percentage = 1.52% homopolymer indels = 48.53% >>>>>>> Coverage mean coverageData = 0.056X std coverageData = 0.4908X There is a 4.6% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 12881045 0.05167908889583067 0.9436494937686246 chr2 243199373 20504996 0.08431352329185487 0.4923955368377618 chr3 198022430 11204038 0.05657964100329443 0.27580210152242907 chr4 191154276 14270642 0.07465510214377837 0.3318402140108329 chr5 180915260 11146669 0.061612652243929006 0.29421596103618003 chr6 171115067 10871302 0.06353211432865816 0.3007014833862369 chr7 159138663 12797174 0.08041524139234474 0.5095114930357773 chr8 146364022 7249339 0.049529514842110586 1.082447811674695 chr9 141213431 12757765 0.09034384979995282 0.46020517983068954 chr10 135534747 6166815 0.04549988203394072 0.39674535620733153 chr11 135006516 7247286 0.05368100899663243 0.38257582066185175 chr12 133851895 6352983 0.04746277966404585 0.25299235133438336 chr13 115169878 4811763 0.04177970041784711 0.2346526204146357 chr14 107349540 2899686 0.027011629486255833 0.2018917902692954 chr15 102531392 1516792 0.014793440042245793 0.13948469308719 chr16 90354753 4571815 0.05059850033567133 0.2766975969492414 chr17 81195210 3984920 0.04907826459220932 0.270385798577865 chr18 78077248 3859717 0.04943459328894379 0.6978346293115919 chr19 59128983 3250937 0.05498043150852096 0.5368273665350534 chr20 63025520 3605122 0.0572009877903427 0.2877907453724731 chr21 48129895 2069355 0.042995211188389254 0.25473968981609807 chr22 51304566 1514570 0.029521154121058154 0.19513305810175546 chrMT 16571 84427 5.094864522358336 3.443298039036342 chrX 155270560 7398883 0.04765155094436447 0.2748550011059084 chrY 59373566 312935 0.005270611504116158 0.12018949414129082