BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081778.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 = 2,454,988 number of mapped reads = 2,191,547 (89.27%) number of supplementary alignments = 12,388 (0.5%) number of secondary alignments = 0 number of mapped bases = 147,741,190 bp number of sequenced bases = 147,681,516 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,227 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8628 >>>>>>> ACTG content number of A's = 39,997,191 bp (27.08%) number of C's = 29,112,816 bp (19.71%) number of T's = 44,644,631 bp (30.23%) number of G's = 33,925,180 bp (22.97%) number of N's = 1,698 bp (0%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,316,862 number of insertions = 10,618 mapped reads with insertion percentage = 0.48% number of deletions = 32,323 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.23% >>>>>>> Coverage mean coverageData = 0.0477X std coverageData = 0.387X There is a 3.97% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.11% 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 0.01% 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 13842647 0.055537061229628794 0.6897326890754801 chr2 243199373 3481180 0.014314099403537525 0.37537368156688344 chr3 198022430 8943730 0.045165237089555964 0.24924224806604792 chr4 191154276 11163052 0.05839812864034493 0.3129122006743879 chr5 180915260 9597874 0.053051765782499496 0.2675308827001225 chr6 171115067 10049718 0.05873076039528419 0.3361025579933083 chr7 159138663 8399871 0.0527833453018265 0.5312800247969045 chr8 146364022 7964531 0.054415906936473774 0.42106397135476137 chr9 141213431 6829513 0.048363055494346004 0.3715285344393818 chr10 135534747 8170674 0.060284717984532776 0.44857761165787835 chr11 135006516 3573255 0.02646727806826746 0.2584088671941688 chr12 133851895 6798696 0.0507926764876956 0.2623945529627766 chr13 115169878 5583368 0.04847941229910828 0.2547476300907004 chr14 107349540 5327607 0.04962859645229965 0.27267425177982785 chr15 102531392 4975751 0.048529049522706175 0.2588650102555129 chr16 90354753 5324259 0.058926164072409117 0.3125867555012969 chr17 81195210 4759746 0.05862101963896639 0.2951485228633418 chr18 78077248 4035522 0.051686273573576774 0.6562209570659915 chr19 59128983 3670808 0.06208136541093562 0.4926312078861349 chr20 63025520 3725177 0.059105851090161574 0.2912537012524739 chr21 48129895 1528929 0.0317667221173036 0.23824675868203465 chr22 51304566 2081797 0.0405772265961669 0.2342949322386929 chrMT 16571 6600 0.39828616257317 0.6723641736303319 chrX 155270560 7474142 0.048136246819744835 0.2757745211287378 chrY 59373566 432743 0.007288479186175208 0.19089864935624098