BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617669.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,312,896 (94.73%) number of supplementary alignments = 181,677 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,342,070 number of mapped paired reads (second in pair) = 14,970,826 number of mapped paired reads (both in pair) = 29,570,212 number of mapped paired reads (singletons) = 742,684 number of mapped bases = 2,930,976,701 bp number of sequenced bases = 2,929,175,581 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,020,641 duplication rate = 10.81% >>>>>>> Insert size mean insert size = 47,776.6533 std insert size = 2,038,582.9304 median insert size = 224 >>>>>>> Mapping quality mean mapping quality = 52.5557 >>>>>>> ACTG content number of A's = 871,978,870 bp (29.77%) number of C's = 582,972,043 bp (19.9%) number of T's = 871,421,866 bp (29.75%) number of G's = 598,945,656 bp (20.45%) number of N's = 3,857,146 bp (0.13%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0141 number of mismatches = 40,249,537 number of insertions = 462,861 mapped reads with insertion percentage = 1.5% number of deletions = 1,080,032 mapped reads with deletion percentage = 3.49% homopolymer indels = 47.66% >>>>>>> Coverage mean coverageData = 0.9468X std coverageData = 10.6172X There is a 33.28% of reference with a coverageData >= 1X There is a 19.25% of reference with a coverageData >= 2X There is a 11.75% of reference with a coverageData >= 3X There is a 7.5% of reference with a coverageData >= 4X There is a 4.93% of reference with a coverageData >= 5X There is a 3.34% of reference with a coverageData >= 6X There is a 2.32% of reference with a coverageData >= 7X There is a 1.64% of reference with a coverageData >= 8X There is a 1.19% of reference with a coverageData >= 9X There is a 0.88% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.51% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 179851809 0.7215701540819832 10.20252982766625 chr2 243199373 303185145 1.246652658927702 12.18558666041596 chr3 198022430 245349930 1.2390007031021688 2.4875863071600204 chr4 191154276 163903628 0.8574415986383689 8.498858065729678 chr5 180915260 193550229 1.0698391556356275 2.334554750276499 chr6 171115067 142232595 0.8312102346896197 5.735759257826745 chr7 159138663 229373769 1.441345331649544 13.46081679768719 chr8 146364022 129801524 0.8868403739274123 4.086388524555119 chr9 141213431 120387141 0.8525190567744225 20.608615295117097 chr10 135534747 124413177 0.9179430349325844 21.414619987396406 chr11 135006516 161056379 1.1929526349676338 11.93719763752751 chr12 133851895 125114571 0.9347239424589394 2.374355825313428 chr13 115169878 125638096 1.0908937144137636 2.3322648303615297 chr14 107349540 83812204 0.7807411564129665 2.477844781279729 chr15 102531392 62708028 0.6115983288318176 1.7860842157505694 chr16 90354753 81113429 0.8977217723122989 16.630920577028725 chr17 81195210 72429544 0.8920420798221964 12.79967012193594 chr18 78077248 54246197 0.6947759864691953 18.30444202417544 chr19 59128983 31086392 0.5257386551025239 6.102241453744522 chr20 63025520 79419245 1.260112490940178 3.0676954875437508 chr21 48129895 42862319 0.8905550074439181 4.4391152484354555 chr22 51304566 18939504 0.3691582538676967 1.2975630894906411 chrMT 16571 3065139 184.97006819141873 130.47022178514678 chrX 155270560 145565844 0.9374980292464972 4.367681606662655 chrY 59373566 11870863 0.19993515296015738 17.39302044238553