BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234140.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 = 893,417 number of mapped reads = 372,217 (41.66%) number of supplementary alignments = 1,735 (0.19%) number of secondary alignments = 0 number of mapped bases = 22,979,102 bp number of sequenced bases = 22,963,238 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,658 duplication rate = 2.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7586 >>>>>>> ACTG content number of A's = 6,362,867 bp (27.71%) number of C's = 3,989,279 bp (17.37%) number of T's = 7,397,019 bp (32.21%) number of G's = 5,211,160 bp (22.69%) number of N's = 2,913 bp (0.01%) GC percentage = 40.07% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 253,005 number of insertions = 2,064 mapped reads with insertion percentage = 0.55% number of deletions = 9,142 mapped reads with deletion percentage = 2.42% homopolymer indels = 46.56% >>>>>>> Coverage mean coverageData = 0.0074X std coverageData = 0.107X There is a 0.68% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 1931288 0.007748377886689398 0.12683563278577425 chr2 243199373 1652340 0.006794178700452488 0.1100238102386163 chr3 198022430 1850981 0.009347329996909947 0.10440867518133226 chr4 191154276 1221693 0.006391136131320442 0.08752774944978248 chr5 180915260 1369637 0.007570599627693098 0.09381455282621666 chr6 171115067 1455576 0.008506416328610034 0.1042436044656546 chr7 159138663 1404254 0.00882409072394934 0.12603345912009153 chr8 146364022 1172515 0.008010950942575219 0.1721660713158923 chr9 141213431 974977 0.006904279522816778 0.10143958312620358 chr10 135534747 1101459 0.008126764718127965 0.10206755339120299 chr11 135006516 1115018 0.008258993958484196 0.10861707394980097 chr12 133851895 897100 0.00670218378305365 0.08805706689356986 chr13 115169878 873317 0.007582859469556788 0.09468622979504954 chr14 107349540 913877 0.008513096562873022 0.10166369638432252 chr15 102531392 568053 0.005540283701600384 0.07927482636746211 chr16 90354753 594748 0.006582365401408379 0.0899125274299191 chr17 81195210 560815 0.0069069961146722815 0.09142449262950567 chr18 78077248 540135 0.006917956432070966 0.13464837863911858 chr19 59128983 521768 0.008824234301476148 0.10927741496502648 chr20 63025520 528574 0.008386666226633276 0.09905063005618421 chr21 48129895 352624 0.007326506737652347 0.09229569548725514 chr22 51304566 216220 0.004214439705035221 0.06923846154822713 chrMT 16571 15731 0.9493090338543239 1.2613305176390652 chrX 155270560 1064933 0.006858563529364485 0.0916198853925271 chrY 59373566 81469 0.0013721426130948577 0.041710546589554406