BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081739.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 = 2,634,100 number of mapped reads = 2,394,075 (90.89%) number of supplementary alignments = 17,197 (0.65%) number of secondary alignments = 0 number of mapped bases = 161,072,987 bp number of sequenced bases = 161,015,798 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,856 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2931 >>>>>>> ACTG content number of A's = 44,772,686 bp (27.81%) number of C's = 30,287,901 bp (18.81%) number of T's = 50,528,428 bp (31.38%) number of G's = 35,424,928 bp (22%) number of N's = 1,855 bp (0%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,260,092 number of insertions = 11,416 mapped reads with insertion percentage = 0.47% number of deletions = 32,240 mapped reads with deletion percentage = 1.33% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.052X std coverageData = 0.3779X There is a 4.39% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 12481695 0.05007688626781796 0.5701215626848525 chr2 243199373 13699567 0.05633060164180604 0.4530184011058051 chr3 198022430 10874993 0.05491798580595138 0.2719344801652418 chr4 191154276 10924834 0.05715192057749208 0.2920644165036499 chr5 180915260 9879727 0.05460969406339741 0.26799902325003083 chr6 171115067 9487096 0.05544278576006401 0.30930066735123873 chr7 159138663 8809169 0.0553553035694412 0.5036969373582881 chr8 146364022 8378419 0.0572437056970189 0.5379134862232988 chr9 141213431 6763982 0.04789899906900499 0.3556277500468518 chr10 135534747 7394256 0.05455616484826581 0.4061202485672159 chr11 135006516 7338457 0.0543563171425 0.33236654923519887 chr12 133851895 7301020 0.054545510917122245 0.26992935068701024 chr13 115169878 5160985 0.044811934245515134 0.24302205335216756 chr14 107349540 4956053 0.046167435836241125 0.25762178827812804 chr15 102531392 4450885 0.04340997340599843 0.2416920156873848 chr16 90354753 4573578 0.05061801231419447 0.2923249481189009 chr17 81195210 4161771 0.051256361058737335 0.27758611843289 chr18 78077248 4331238 0.05547375337819284 0.6234739490437943 chr19 59128983 2879657 0.04870127734143508 0.4587475544404961 chr20 63025520 3255834 0.051658978775581704 0.26932412399231526 chr21 48129895 2121238 0.04407318985424755 0.262286595920427 chr22 51304566 1640978 0.03198502838909114 0.2027254623318261 chrMT 16571 31653 1.9101442278679621 2.06349875195664 chrX 155270560 9771265 0.06293057099813384 0.3093055402875571 chrY 59373566 404637 0.006815103542879671 0.15853564081595878