BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819111.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,280,535 number of mapped reads = 2,086,297 (91.48%) number of supplementary alignments = 8,062 (0.35%) number of secondary alignments = 0 number of mapped bases = 121,120,370 bp number of sequenced bases = 121,082,006 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,034 duplication rate = 4.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9441 >>>>>>> ACTG content number of A's = 29,732,966 bp (24.56%) number of C's = 24,640,680 bp (20.35%) number of T's = 38,975,555 bp (32.19%) number of G's = 27,730,899 bp (22.9%) number of N's = 1,906 bp (0%) GC percentage = 43.25% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 616,603 number of insertions = 9,171 mapped reads with insertion percentage = 0.44% number of deletions = 23,364 mapped reads with deletion percentage = 1.11% homopolymer indels = 42.8% >>>>>>> Coverage mean coverageData = 0.0391X std coverageData = 0.3558X There is a 3.37% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% 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 12002048 0.04815252997905269 0.7002723507607483 chr2 243199373 9618724 0.03955077630895044 0.4219949829115044 chr3 198022430 6636500 0.03351388022053865 0.20975466435731294 chr4 191154276 6688966 0.03499249998467207 0.2511935234096346 chr5 180915260 6503838 0.03594963741588189 0.21529660415638321 chr6 171115067 5178183 0.030261408833156696 0.2663301783235723 chr7 159138663 6130089 0.038520425422953315 0.4371117802626079 chr8 146364022 11161375 0.07625764069260135 0.3802108436155845 chr9 141213431 5052897 0.03578198592172157 0.2922283720510991 chr10 135534747 6281012 0.046342448257936396 0.3605664291145072 chr11 135006516 4079737 0.030218815512578667 0.3122832504961028 chr12 133851895 5669627 0.04235746531642305 0.23383370334425949 chr13 115169878 2960197 0.025702875191028682 0.18173507044503834 chr14 107349540 2884101 0.026866449544171313 0.1914435208056285 chr15 102531392 3155885 0.030779695256648813 0.2034761532576108 chr16 90354753 3780514 0.04184078727988997 0.2490510869775092 chr17 81195210 4314216 0.05313387329129391 0.277981962847242 chr18 78077248 2841451 0.03639281702141961 0.5525142314214908 chr19 59128983 2453992 0.04150235426846425 0.458682883879567 chr20 63025520 3439321 0.054570291526353135 0.26796253139401494 chr21 48129895 1653677 0.03435862471754821 0.23560824537275854 chr22 51304566 1004268 0.019574632012285223 0.1569375906821328 chrMT 16571 50777 3.0642085571178566 2.3455529715675603 chrX 155270560 7163703 0.04613690451042361 0.27396622953159205 chrY 59373566 415272 0.006994223658386966 0.20507226153536792