BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013299.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 = 2,117,951 number of mapped reads = 1,901,970 (89.8%) number of supplementary alignments = 10,222 (0.48%) number of secondary alignments = 0 number of mapped bases = 126,838,767 bp number of sequenced bases = 126,791,492 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,123 duplication rate = 2.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1307 >>>>>>> ACTG content number of A's = 35,661,860 bp (28.13%) number of C's = 23,305,303 bp (18.38%) number of T's = 39,947,096 bp (31.51%) number of G's = 27,850,573 bp (21.97%) number of N's = 26,660 bp (0.02%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 976,498 number of insertions = 8,732 mapped reads with insertion percentage = 0.46% number of deletions = 26,842 mapped reads with deletion percentage = 1.4% homopolymer indels = 45.92% >>>>>>> Coverage mean coverageData = 0.041X std coverageData = 0.3841X There is a 3.57% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 9034202 0.03624545432927928 0.7191824156604737 chr2 243199373 16091236 0.06616479229163144 0.44246855917133504 chr3 198022430 6835397 0.03451829674042481 0.2042206728472238 chr4 191154276 8562004 0.04479106708551997 0.2439953357936515 chr5 180915260 6042785 0.033401190148360065 0.20401178803384185 chr6 171115067 6468702 0.037803228630942244 0.2823886386460648 chr7 159138663 8074847 0.05074095036226363 0.659768775162736 chr8 146364022 8997816 0.06147559951584276 0.4739148689886271 chr9 141213431 4246465 0.030071254341238973 0.32139818033735174 chr10 135534747 6348817 0.0468427258730929 0.36638806090276776 chr11 135006516 4509250 0.03340023973361404 0.28724201060545057 chr12 133851895 6239799 0.0466171883483607 0.2434613941313363 chr13 115169878 3905701 0.03391252181408059 0.20120887533455062 chr14 107349540 3742965 0.0348670800079814 0.2207635152611828 chr15 102531392 2201845 0.02147483767703066 0.16648239803171336 chr16 90354753 3258130 0.0360593094643289 0.22282982012486732 chr17 81195210 3072229 0.03783756455584018 0.2634156453907736 chr18 78077248 2535349 0.03247231511028668 0.5821232656016762 chr19 59128983 2236132 0.03781786674734453 0.4737761128365621 chr20 63025520 3336666 0.05294150686896355 0.2666161764346817 chr21 48129895 2838222 0.05897004346259222 0.2871125726117548 chr22 51304566 885320 0.01725616390556739 0.14234989870180964 chrMT 16571 17875 1.0786916903023354 1.1585087849147084 chrX 155270560 7068392 0.04552306631727225 0.2783967036246757 chrY 59373566 288621 0.004861102666462715 0.10331202579401187