BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472804.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 = 2,190,198 number of mapped reads = 1,681,476 (76.77%) number of supplementary alignments = 16,938 (0.77%) number of secondary alignments = 0 number of mapped bases = 105,215,048 bp number of sequenced bases = 105,168,065 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,006 duplication rate = 3.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6107 >>>>>>> ACTG content number of A's = 27,955,735 bp (26.58%) number of C's = 21,091,071 bp (20.05%) number of T's = 30,961,110 bp (29.44%) number of G's = 25,158,026 bp (23.92%) number of N's = 2,123 bp (0%) GC percentage = 43.98% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 940,488 number of insertions = 8,352 mapped reads with insertion percentage = 0.49% number of deletions = 26,012 mapped reads with deletion percentage = 1.53% homopolymer indels = 45.27% >>>>>>> Coverage mean coverageData = 0.034X std coverageData = 0.2887X There is a 2.78% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 8564298 0.03436018721092775 0.34527681119326403 chr2 243199373 8865871 0.03645515566357978 0.37495858907472585 chr3 198022430 7177441 0.036245596016572464 0.23111320528227725 chr4 191154276 5098943 0.026674490922714175 0.2260442504404811 chr5 180915260 6054829 0.03346776275257267 0.22503171783525192 chr6 171115067 7005344 0.040939375607409255 0.26432981022547153 chr7 159138663 5845271 0.036730678075383855 0.3678204601658741 chr8 146364022 5305518 0.036248785237672686 0.2760676501891269 chr9 141213431 4591405 0.03251393983905115 0.3009377235259001 chr10 135534747 5038950 0.03717828904790002 0.2868833983953906 chr11 135006516 4133840 0.030619559132982886 0.30006207125380696 chr12 133851895 5065743 0.037845881823339145 0.25177810383830607 chr13 115169878 4846266 0.04207928395999516 0.25285613452234035 chr14 107349540 2887543 0.02689851302576611 0.23706229738178738 chr15 102531392 2709685 0.02642785733368372 0.2291456165053938 chr16 90354753 3186524 0.035266811033172765 0.25081456755406073 chr17 81195210 2790681 0.03437002010340265 0.25066709193387726 chr18 78077248 2268636 0.029056300754862673 0.4786059086304743 chr19 59128983 2436647 0.04120901250745341 0.3110019028579807 chr20 63025520 3326641 0.05278244431779381 0.29813538895273134 chr21 48129895 1449298 0.030112220273906684 0.23456198220250304 chr22 51304566 1210845 0.023601115736950198 0.19873716907305267 chrMT 16571 132394 7.989499728441253 5.446716152905492 chrX 155270560 4739065 0.030521336433642025 0.24274262934266258 chrY 59373566 483370 0.008141165043042893 0.13876053624235438