BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708575.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,534,938 number of mapped reads = 3,740,618 (82.48%) number of supplementary alignments = 98 (0%) number of secondary alignments = 0 number of mapped bases = 186,513,344 bp number of sequenced bases = 186,495,989 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,239 duplication rate = 0.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6072 >>>>>>> ACTG content number of A's = 57,696,025 bp (30.94%) number of C's = 35,487,495 bp (19.03%) number of T's = 57,426,106 bp (30.79%) number of G's = 35,877,458 bp (19.24%) number of N's = 8,905 bp (0%) GC percentage = 38.27% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 301,104 number of insertions = 12,906 mapped reads with insertion percentage = 0.34% number of deletions = 10,226 mapped reads with deletion percentage = 0.27% homopolymer indels = 47.58% >>>>>>> Coverage mean coverageData = 0.0602X std coverageData = 0.2789X There is a 5.17% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.12% 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 37370208 0.14993025032423088 0.45681002299411866 chr2 243199373 9728171 0.04000080625207862 0.2182649112827639 chr3 198022430 9838313 0.04968282128443732 0.24105197740348333 chr4 191154276 7421124 0.038822694188645826 0.210387688528308 chr5 180915260 14199764 0.0784884812922912 0.31693392616370814 chr6 171115067 7352166 0.04296621056753582 0.22587154267296355 chr7 159138663 4943134 0.03106180425808906 0.18848242196814366 chr8 146364022 8431336 0.05760524946492657 0.2626981110092442 chr9 141213431 9522986 0.06743682900814159 0.29632025306876003 chr10 135534747 4723262 0.03484908560016717 0.20555587382201593 chr11 135006516 17640124 0.13066127860080473 0.4115359827445464 chr12 133851895 3724638 0.027826561588836677 0.18073997457391103 chr13 115169878 3972202 0.03448993841948847 0.20016961192551505 chr14 107349540 9296671 0.08660187086036884 0.3368831481037597 chr15 102531392 8337240 0.08131402331882903 0.3263650497049725 chr16 90354753 9185076 0.10165570371267575 0.360247131526571 chr17 81195210 4994500 0.061512249306332235 0.27474117911149726 chr18 78077248 2921309 0.037415624587587924 0.2124841487416815 chr19 59128983 1123247 0.01899655537792693 0.14492095447107017 chr20 63025520 1732469 0.027488372963840678 0.1801399463498095 chr21 48129895 1270398 0.02639519575099842 0.17560231879386778 chr22 51304566 672703 0.013111951867987734 0.12166999767885979 chrMT 16571 100 0.006034638826866212 0.07744818888195831 chrX 155270560 7904826 0.050910011530840106 0.2549024249285472 chrY 59373566 207377 0.0034927496185760513 0.06200119826487669