BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094082.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 334,674 number of mapped reads = 324,611 (96.99%) number of supplementary alignments = 11,701 (3.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 163,033 number of mapped paired reads (second in pair) = 161,578 number of mapped paired reads (both in pair) = 322,584 number of mapped paired reads (singletons) = 2,027 number of mapped bases = 44,092,285 bp number of sequenced bases = 43,077,996 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 308,389 duplication rate = 49.22% >>>>>>> Insert size mean insert size = 490,804.7221 std insert size = 6,388,210.8569 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 38.5088 >>>>>>> ACTG content number of A's = 11,193,340 bp (25.98%) number of C's = 10,345,963 bp (24.02%) number of T's = 10,812,154 bp (25.1%) number of G's = 10,725,964 bp (24.9%) number of N's = 575 bp (0%) GC percentage = 48.92% >>>>>>> Mismatches and indels general error rate = 0.0409 number of mismatches = 1,710,680 number of insertions = 24,191 mapped reads with insertion percentage = 7.3% number of deletions = 130,066 mapped reads with deletion percentage = 38.14% homopolymer indels = 27.13% >>>>>>> Coverage mean coverageData = 0.0142X std coverageData = 4.1927X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 214558 8.608122986381646E-4 0.33911081152361416 chr2 243199373 2325184 0.00956081412265812 4.308062270946111 chr3 198022430 919659 0.004644216314283185 2.064565660255008 chr4 191154276 662429 0.0034654155473874933 1.5500608948983339 chr5 180915260 294522 0.0016279555411743598 0.7498958956021013 chr6 171115067 869737 0.005082761063933663 2.8587775101459463 chr7 159138663 1507326 0.009471777452346699 3.76688395899727 chr8 146364022 713757 0.00487658777236936 2.0088233960040442 chr9 141213431 611766 0.004332208315227466 2.3488375678808735 chr10 135534747 866063 0.006389970241358107 2.3187378829478558 chr11 135006516 1477193 0.010941642253770922 3.6591393187293897 chr12 133851895 1611621 0.012040330097679977 4.484269659884961 chr13 115169878 961223 0.00834613196342884 2.4276028531848706 chr14 107349540 239747 0.002233330482832064 0.898690625299974 chr15 102531392 818828 0.007986119997278492 2.500653216256555 chr16 90354753 418043 0.004626685217101971 1.8418078764870873 chr17 81195210 913293 0.01124811426683914 3.8804672171629915 chr18 78077248 99577 0.001275365135820361 0.4483741501284773 chr19 59128983 158069 0.0026732913704942294 0.6304651190535014 chr20 63025520 278039 0.004411530440367648 1.2666605140471923 chr21 48129895 906521 0.018834884223204725 8.514125072057842 chr22 51304566 61533 0.0011993669335395997 0.310458215370578 chrMT 16571 1327046 80.082433166375 415.2126067481521 chrX 155270560 25577176 0.1647265006321868 13.580149216095968 chrY 59373566 259375 0.004368526559445663 0.8652456163099574