BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472376.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,327,972 number of mapped reads = 17,160,849 (99.04%) number of supplementary alignments = 61,792 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,602,434 number of mapped paired reads (second in pair) = 8,558,415 number of mapped paired reads (both in pair) = 17,066,934 number of mapped paired reads (singletons) = 93,915 number of mapped bases = 1,684,287,725 bp number of sequenced bases = 1,684,103,290 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,432,649 duplication rate = 47.15% >>>>>>> Insert size mean insert size = 18,717.1855 std insert size = 1,348,954.4066 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 54.8681 >>>>>>> ACTG content number of A's = 451,207,148 bp (26.79%) number of C's = 392,424,073 bp (23.3%) number of T's = 451,269,229 bp (26.8%) number of G's = 388,998,254 bp (23.1%) number of N's = 204,586 bp (0.01%) GC percentage = 46.4% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 9,435,718 number of insertions = 98,359 mapped reads with insertion percentage = 0.57% number of deletions = 79,740 mapped reads with deletion percentage = 0.46% homopolymer indels = 46.51% >>>>>>> Coverage mean coverageData = 0.5441X std coverageData = 15.5487X There is a 4.78% of reference with a coverageData >= 1X There is a 2.03% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.32% of reference with a coverageData >= 17X There is a 0.31% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.3% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.28% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.27% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.26% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.23% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.22% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 160292996 0.6430996855971725 18.248286949920715 chr2 243199373 126928698 0.5219121103572911 14.782295529324637 chr3 198022430 101904887 0.5146128496655656 12.109081088838016 chr4 191154276 45676756 0.23895231095955186 10.897160061864533 chr5 180915260 68811611 0.38035271872588305 12.125128313680971 chr6 171115067 127901063 0.7474564644853863 15.930948685648469 chr7 159138663 128421232 0.8069769443771184 20.163945555296166 chr8 146364022 76892512 0.5253511822734688 13.56917832543119 chr9 141213431 67178413 0.47572254653312684 13.539118430985745 chr10 135534747 52624685 0.3882744917065437 10.870940085579514 chr11 135006516 61809429 0.45782552451023917 15.028174539565399 chr12 133851895 89854672 0.6712992147029372 15.289888247731518 chr13 115169878 53959029 0.46851685472828236 15.343963141838115 chr14 107349540 29277386 0.2727294965586252 9.996290070879462 chr15 102531392 28286596 0.2758822975894056 8.43892752805472 chr16 90354753 96766766 1.0709648666739202 26.438927349366814 chr17 81195210 67683492 0.8335897154524263 17.283937923363553 chr18 78077248 23526978 0.30132949870364284 12.079467089129471 chr19 59128983 62376156 1.0549167740632373 23.340693149713697 chr20 63025520 53620035 0.8507670384948827 22.103532921931937 chr21 48129895 14101510 0.2929885884853894 11.565711849647085 chr22 51304566 19289313 0.3759765358896126 15.382430010200329 chrMT 16571 8027 0.4844004586325508 0.8471581320441008 chrX 155270560 126756047 0.8163559595585924 21.153810075860587 chrY 59373566 339436 0.005716954915593246 0.37992796634697895