BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080964.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 = 6,499,691 number of mapped reads = 5,737,156 (88.27%) number of supplementary alignments = 59,873 (0.92%) number of secondary alignments = 0 number of mapped bases = 385,491,429 bp number of sequenced bases = 385,347,818 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 453,368 duplication rate = 6.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9384 >>>>>>> ACTG content number of A's = 108,104,674 bp (28.05%) number of C's = 67,915,475 bp (17.62%) number of T's = 125,222,206 bp (32.5%) number of G's = 83,348,762 bp (21.63%) number of N's = 756,701 bp (0.2%) GC percentage = 39.25% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 3,850,507 number of insertions = 30,863 mapped reads with insertion percentage = 0.53% number of deletions = 86,716 mapped reads with deletion percentage = 1.5% homopolymer indels = 49.02% >>>>>>> Coverage mean coverageData = 0.1245X std coverageData = 0.8095X There is a 8.14% of reference with a coverageData >= 1X There is a 2.61% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 31860460 0.12782499747513168 1.0772626387971127 chr2 243199373 25716246 0.10574141570669263 0.7748690032818276 chr3 198022430 33274021 0.16803157601893887 0.5831374851574459 chr4 191154276 23828051 0.12465350762020097 0.5408096671951107 chr5 180915260 21543478 0.11908049105420958 0.48688525201698835 chr6 171115067 32582898 0.19041513159095452 0.9200344745027106 chr7 159138663 18894678 0.11873090827714193 0.7226303872152429 chr8 146364022 32662938 0.2231623424505238 1.6393522126384128 chr9 141213431 19774446 0.14003233162715237 1.0298848393000863 chr10 135534747 16947040 0.12503834164385905 0.6700500835934514 chr11 135006516 17094359 0.1266187700155154 0.6336667742085678 chr12 133851895 18985332 0.1418383505142008 0.5622568838657885 chr13 115169878 10308372 0.08950579942439463 0.41708299803589804 chr14 107349540 10829506 0.10088078626140363 0.604912794172281 chr15 102531392 9508395 0.0927364274933476 0.4264243525221406 chr16 90354753 8796433 0.09735440259573284 0.5754785865754265 chr17 81195210 7507737 0.09246526981086692 0.44629895812589143 chr18 78077248 9733888 0.12466996787591694 1.771564277087623 chr19 59128983 6944012 0.11743838043011834 0.899164793442914 chr20 63025520 6009908 0.09535673803246685 0.48513135662693524 chr21 48129895 7212407 0.1498529552162954 0.6760406096813713 chr22 51304566 3071865 0.0598750801244474 0.334266677835079 chrMT 16571 99981 6.033492245489107 4.351949605975714 chrX 155270560 11482942 0.07395440578046476 0.43556170733215055 chrY 59373566 822036 0.013845151224368097 0.2716960476097648