BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548932.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,105,994 number of mapped reads = 8,809,236 (87.17%) number of secondary alignments = 0 number of mapped bases = 348,814,726 bp number of sequenced bases = 348,775,636 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 367,213 duplication rate = 3.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0948 >>>>>>> ACTG content number of A's = 101,874,768 bp (29.21%) number of C's = 72,191,552 bp (20.7%) number of T's = 102,503,352 bp (29.39%) number of G's = 72,202,842 bp (20.7%) number of N's = 3,122 bp (0%) GC percentage = 41.4% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 941,339 number of insertions = 11,036 mapped reads with insertion percentage = 0.13% number of deletions = 29,065 mapped reads with deletion percentage = 0.33% homopolymer indels = 41.13% >>>>>>> Coverage mean coverageData = 0.1127X std coverageData = 1.2846X There is a 8.6% of reference with a coverageData >= 1X There is a 1.87% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 27119406 0.10880376502652725 1.1698136640270709 chr2 243199373 29547612 0.1214954283619802 0.6236983825064495 chr3 198022430 23975233 0.12107331982543594 0.4335040771229276 chr4 191154276 23174474 0.1212344002181777 0.44677225840136364 chr5 180915260 21510209 0.118896598330069 0.4367670965070185 chr6 171115067 20643768 0.12064260828650467 0.49684063361976305 chr7 159138663 19316936 0.12138430495674078 0.9473578245926807 chr8 146364022 18372846 0.125528430750557 5.138563506612263 chr9 141213431 14359008 0.10168301908902702 0.6162936934303329 chr10 135534747 16175938 0.11934901092190034 0.5601281845290016 chr11 135006516 15875073 0.11758745777870455 0.7086978829106874 chr12 133851895 15847149 0.11839316133701357 0.4441148297096048 chr13 115169878 11537322 0.10017655831848671 0.3904786063180673 chr14 107349540 10835760 0.10093904454550993 0.4846736709687464 chr15 102531392 9949960 0.09704305974895962 0.38719497201077885 chr16 90354753 9459473 0.10469258877836786 0.44756714467400727 chr17 81195210 8833146 0.1087890036863012 0.44172216594642666 chr18 78077248 9397282 0.12035877596505451 1.057062969027883 chr19 59128983 6483766 0.10965461726273898 1.048962886788214 chr20 63025520 6974608 0.11066323609864702 0.43275121604699257 chr21 48129895 4426099 0.09196153450989245 0.42569764174557456 chr22 51304566 3745615 0.07300743953276985 0.40125343565436866 chrMT 16571 13286 0.801762114537445 1.1690753740850868 chrX 155270560 20210754 0.1301647524166848 0.5440441286212785 chrY 59373566 1030003 0.017347837925045635 0.22013224705870418