BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082783.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 = 3,988,084 number of mapped reads = 3,384,778 (84.87%) number of supplementary alignments = 25,441 (0.64%) number of secondary alignments = 0 number of mapped bases = 229,131,649 bp number of sequenced bases = 229,045,751 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 194,947 duplication rate = 4.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1975 >>>>>>> ACTG content number of A's = 64,996,512 bp (28.38%) number of C's = 41,208,117 bp (17.99%) number of T's = 74,904,277 bp (32.7%) number of G's = 47,924,069 bp (20.92%) number of N's = 12,776 bp (0.01%) GC percentage = 38.91% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 2,022,335 number of insertions = 18,447 mapped reads with insertion percentage = 0.54% number of deletions = 50,751 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.94% >>>>>>> Coverage mean coverageData = 0.074X std coverageData = 0.5556X There is a 5.64% of reference with a coverageData >= 1X There is a 1.22% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% 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% 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 21497386 0.08624807398172941 1.044925856498874 chr2 243199373 23640921 0.0972079849893363 0.6633531434663706 chr3 198022430 16768171 0.08467813974406839 0.36033412537397597 chr4 191154276 13389263 0.07004427669721602 0.34085291777266163 chr5 180915260 13137887 0.07261900958492944 0.33757619400592315 chr6 171115067 16774685 0.09803160700045192 0.5720202473085906 chr7 159138663 11559545 0.07263819352309124 0.46283920862937034 chr8 146364022 17817173 0.12173191715106052 0.8366568911675034 chr9 141213431 6856340 0.0485530303417102 0.4649467834317436 chr10 135534747 8513955 0.06281750760194359 0.44201228376048124 chr11 135006516 9463990 0.07010024612441669 0.446231792234595 chr12 133851895 6965596 0.052039577026533695 0.2925218519737405 chr13 115169878 5415302 0.047020124480812595 0.26864375587064626 chr14 107349540 4851083 0.04518960211659966 0.30985005207087324 chr15 102531392 4318932 0.04212302121090875 0.25288933910569666 chr16 90354753 8887518 0.09836248459447396 0.4384924181289419 chr17 81195210 5305581 0.06534352211171078 0.37231448359883434 chr18 78077248 9099384 0.11654334947871113 1.0817510655733522 chr19 59128983 3125545 0.05285977944183481 0.6723100094769657 chr20 63025520 4397988 0.06978106646323584 0.34506192979584854 chr21 48129895 4604164 0.09566121014807949 0.39671389091300735 chr22 51304566 2800665 0.054589000908808 0.2863835965876494 chrMT 16571 281678 16.99824995474021 10.09013627378281 chrX 155270560 9256520 0.05961542226678387 0.3549320179297557 chrY 59373566 402377 0.0067770394656773685 0.13275418898150773