BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617671.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 = 30,386,775 (94.96%) number of supplementary alignments = 156,106 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,385,150 number of mapped paired reads (second in pair) = 15,001,625 number of mapped paired reads (both in pair) = 29,642,822 number of mapped paired reads (singletons) = 743,953 number of mapped bases = 2,943,277,349 bp number of sequenced bases = 2,941,495,852 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,986,058 duplication rate = 10.73% >>>>>>> Insert size mean insert size = 45,451.5482 std insert size = 2,004,715.3768 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 52.5927 >>>>>>> ACTG content number of A's = 869,874,906 bp (29.57%) number of C's = 584,860,049 bp (19.88%) number of T's = 871,965,540 bp (29.64%) number of G's = 605,587,542 bp (20.59%) number of N's = 9,207,815 bp (0.31%) GC percentage = 40.47% >>>>>>> Mismatches and indels general error rate = 0.0184 number of mismatches = 53,227,782 number of insertions = 462,088 mapped reads with insertion percentage = 1.49% number of deletions = 1,078,875 mapped reads with deletion percentage = 3.48% homopolymer indels = 47.18% >>>>>>> Coverage mean coverageData = 0.9508X std coverageData = 10.2147X There is a 33.39% of reference with a coverageData >= 1X There is a 19.34% of reference with a coverageData >= 2X There is a 11.83% of reference with a coverageData >= 3X There is a 7.56% of reference with a coverageData >= 4X There is a 4.98% of reference with a coverageData >= 5X There is a 3.38% of reference with a coverageData >= 6X There is a 2.35% of reference with a coverageData >= 7X There is a 1.67% of reference with a coverageData >= 8X There is a 1.21% of reference with a coverageData >= 9X There is a 0.89% of reference with a coverageData >= 10X There is a 0.67% of reference with a coverageData >= 11X There is a 0.51% of reference with a coverageData >= 12X There is a 0.4% 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 180741268 0.7251386868159498 10.080149353805579 chr2 243199373 303563942 1.2482102163972273 11.765934653345825 chr3 198022430 246182852 1.2432069033795818 2.4940318851861973 chr4 191154276 164459785 0.8603510653353106 7.942510721169546 chr5 180915260 194907518 1.0773415023143984 2.343745577180637 chr6 171115067 143027822 0.8358575577684226 5.7418343002458085 chr7 159138663 230396598 1.4477726132460973 13.167192120552393 chr8 146364022 130906395 0.8943891621125306 4.127051953703105 chr9 141213431 120388964 0.8525319663113348 18.840007005978922 chr10 135534747 124316578 0.91723030995144 20.79843790370133 chr11 135006516 161661633 1.1974357815440553 11.642000321951134 chr12 133851895 125923137 0.9407646936937277 2.1894825305509187 chr13 115169878 126430628 1.0977751317927071 2.319901772275851 chr14 107349540 84323310 0.7855022946535216 2.494190156822418 chr15 102531392 63293874 0.617312149629257 1.7222935435161963 chr16 90354753 81556064 0.9026206291549488 16.510896190722708 chr17 81195210 72812627 0.8967601290765798 12.389445555293271 chr18 78077248 54094281 0.6928302723989452 17.97998423975253 chr19 59128983 31494767 0.5326451665843804 6.0359037943901725 chr20 63025520 80116244 1.2711714873594062 3.023220464861746 chr21 48129895 42865041 0.8906115627303987 4.284119296351686 chr22 51304566 19119215 0.37266108049720176 1.284373346794902 chrMT 16571 3121831 188.39122563514573 133.22414132054917 chrX 155270560 146133165 0.9411517869195551 4.300784295443919 chrY 59373566 11439810 0.19267513761932373 15.756532489950946