BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082904.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 = 1,742,065 number of mapped reads = 1,547,957 (88.86%) number of supplementary alignments = 19,614 (1.13%) number of secondary alignments = 0 number of mapped bases = 102,280,415 bp number of sequenced bases = 102,242,183 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,685 duplication rate = 4.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0021 >>>>>>> ACTG content number of A's = 27,860,481 bp (27.25%) number of C's = 18,829,320 bp (18.42%) number of T's = 32,706,014 bp (31.99%) number of G's = 22,841,441 bp (22.34%) number of N's = 4,927 bp (0%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 726,497 number of insertions = 8,456 mapped reads with insertion percentage = 0.54% number of deletions = 23,398 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.91% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.2773X There is a 2.65% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 9431926 0.03784113340283313 0.444630038602137 chr2 243199373 10432956 0.042898778361570855 0.42801585389764346 chr3 198022430 6688165 0.03377478500794077 0.2226134390052266 chr4 191154276 5993490 0.03135420313590055 0.2164728707837403 chr5 180915260 5403226 0.02986605994430763 0.20898136310771268 chr6 171115067 6374153 0.03725068231425816 0.2669962424061612 chr7 159138663 5067226 0.03184157705283725 0.22776651899993336 chr8 146364022 9425633 0.06439856510638933 0.3579600581595026 chr9 141213431 3147917 0.022291909329786058 0.2187363092988358 chr10 135534747 3799977 0.028036921041362184 0.22118998318046876 chr11 135006516 3641264 0.02697102412449485 0.21332417311991062 chr12 133851895 3235668 0.024173494144404905 0.19030547061783581 chr13 115169878 2455643 0.02132192065011999 0.17690333626024557 chr14 107349540 2492432 0.023217910388810235 0.19404738284784387 chr15 102531392 1435113 0.013996815726446003 0.14673972226452062 chr16 90354753 4856911 0.053753796438356705 0.28652485641286524 chr17 81195210 2686490 0.03308680401220712 0.22706381937469505 chr18 78077248 2815456 0.03605987752027325 0.3377745267778411 chr19 59128983 2238329 0.03785502280666657 0.32461983542871287 chr20 63025520 2330874 0.03698301894216819 0.23688771501606604 chr21 48129895 2513112 0.052215198059335055 0.2822953900617641 chr22 51304566 1482645 0.028898889818110927 0.20694156549142287 chrMT 16571 74497 4.495624886850522 3.8464605389573188 chrX 155270560 4059267 0.026143185160148838 0.2048622882759618 chrY 59373566 198045 0.0033355752962522076 0.07324569561680684