BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231875.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,463,111 number of mapped reads = 4,225,846 (94.68%) number of supplementary alignments = 31,204 (0.7%) number of secondary alignments = 0 number of mapped bases = 282,670,159 bp number of sequenced bases = 282,551,531 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 346,112 duplication rate = 6.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6836 >>>>>>> ACTG content number of A's = 78,677,683 bp (27.85%) number of C's = 51,555,338 bp (18.25%) number of T's = 90,572,030 bp (32.06%) number of G's = 61,630,607 bp (21.81%) number of N's = 115,873 bp (0.04%) GC percentage = 40.06% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,806,199 number of insertions = 19,855 mapped reads with insertion percentage = 0.47% number of deletions = 67,109 mapped reads with deletion percentage = 1.57% homopolymer indels = 45.08% >>>>>>> Coverage mean coverageData = 0.0913X std coverageData = 1.0321X There is a 7.21% of reference with a coverageData >= 1X There is a 1.32% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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% 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 30975709 0.12427535336010256 2.506944461527532 chr2 243199373 21882979 0.08997958641941071 0.8827808390488101 chr3 198022430 22070856 0.11145634360713581 0.4014204392136007 chr4 191154276 15216817 0.07960489986632577 0.3987801955041774 chr5 180915260 18727553 0.10351560725170447 0.39775310232653127 chr6 171115067 22997164 0.1343959033134119 0.6905110656796436 chr7 159138663 15180539 0.09539189731661878 1.2207952029255196 chr8 146364022 16885705 0.11536786683820427 1.8907133006253298 chr9 141213431 7476227 0.05294274735099383 0.5877487707820386 chr10 135534747 11188186 0.08254847002444325 0.7730326725566554 chr11 135006516 8393333 0.06216983630627132 0.5649927803168489 chr12 133851895 12582910 0.0940062148541117 0.38022989423017217 chr13 115169878 5527127 0.04799108148747019 0.2768366085161044 chr14 107349540 13856368 0.12907710643194187 0.4579321356825209 chr15 102531392 4454450 0.043444743245073664 0.27971007809069776 chr16 90354753 6035414 0.06679686236317861 0.39889713304603913 chr17 81195210 8121046 0.10001878189612416 0.45077529724392923 chr18 78077248 5949092 0.07619494990397202 1.4608182899195044 chr19 59128983 5957082 0.10074724268469153 1.3676981495363014 chr20 63025520 4991272 0.07919445964111045 0.37362738693660336 chr21 48129895 6928681 0.14395794962777292 0.49026068625396035 chr22 51304566 2253897 0.04393170385653394 0.24389703254256895 chrMT 16571 337484 20.365940498461168 11.555897554340207 chrX 155270560 13943000 0.08979809179537962 0.4463561409297531 chrY 59373566 737268 0.0124174451640651 0.2334412978013489