BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085106.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 = 2,178,902 number of mapped reads = 1,872,079 (85.92%) number of supplementary alignments = 14,780 (0.68%) number of secondary alignments = 0 number of mapped bases = 117,965,787 bp number of sequenced bases = 117,927,393 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,500 duplication rate = 2.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8163 >>>>>>> ACTG content number of A's = 34,846,622 bp (29.55%) number of C's = 22,729,026 bp (19.27%) number of T's = 34,801,594 bp (29.51%) number of G's = 25,547,563 bp (21.66%) number of N's = 2,588 bp (0%) GC percentage = 40.94% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 997,703 number of insertions = 9,413 mapped reads with insertion percentage = 0.5% number of deletions = 23,716 mapped reads with deletion percentage = 1.25% homopolymer indels = 45.8% >>>>>>> Coverage mean coverageData = 0.0381X std coverageData = 0.286X There is a 3.41% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% 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% 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 10184700 0.0408612823476175 0.37301753955931166 chr2 243199373 11509831 0.04732672974448828 0.3148461597355876 chr3 198022430 6968824 0.035192094148122514 0.21045520809867949 chr4 191154276 7174701 0.0375335626810671 0.22161487488510231 chr5 180915260 6993217 0.038654655223666595 0.21275261928462078 chr6 171115067 6633798 0.03876805307857548 0.2440505710277468 chr7 159138663 9310972 0.05850854735407699 0.31634185687575733 chr8 146364022 6198642 0.042350858601029696 0.43025307267191426 chr9 141213431 4258275 0.030154886612733033 0.2640424041978596 chr10 135534747 6633771 0.048945168282197034 0.4405489775681995 chr11 135006516 4395653 0.03255882108682814 0.25387270724777 chr12 133851895 5387941 0.040253005009753505 0.21920772702194616 chr13 115169878 3065135 0.02661403357568895 0.1757198910879699 chr14 107349540 3946721 0.036765141238611736 0.2189653023856372 chr15 102531392 3073817 0.02997927698084895 0.18678353503029288 chr16 90354753 3369075 0.03728719174297339 0.2354747637402997 chr17 81195210 2170919 0.026737032886545893 0.1875170632372141 chr18 78077248 2826203 0.03619752325286875 0.5169894000066678 chr19 59128983 1746056 0.029529613252438316 0.31489875666601364 chr20 63025520 2080004 0.033002567848706366 0.20469485833190423 chr21 48129895 1752922 0.036420648746480745 0.22161767742184357 chr22 51304566 887145 0.01729173578819476 0.14194118967373856 chrMT 16571 33275 2.008026069639732 1.788531528223275 chrX 155270560 7048062 0.045392133576384344 0.24803089339547565 chrY 59373566 316128 0.005324389645048438 0.11006892395941394