BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238336.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,425,954 number of mapped reads = 2,155,130 (88.84%) number of supplementary alignments = 18,910 (0.78%) number of secondary alignments = 0 number of mapped bases = 142,459,945 bp number of sequenced bases = 142,391,134 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,310 duplication rate = 3.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8152 >>>>>>> ACTG content number of A's = 39,636,891 bp (27.84%) number of C's = 27,389,253 bp (19.24%) number of T's = 43,764,400 bp (30.74%) number of G's = 31,558,869 bp (22.16%) number of N's = 41,721 bp (0.03%) GC percentage = 41.4% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,222,177 number of insertions = 11,603 mapped reads with insertion percentage = 0.53% number of deletions = 40,072 mapped reads with deletion percentage = 1.84% homopolymer indels = 46.13% >>>>>>> Coverage mean coverageData = 0.046X std coverageData = 0.4154X There is a 3.73% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 11794483 0.04731977377901899 0.6834006265843549 chr2 243199373 13446767 0.055291125277695516 0.5211730473449668 chr3 198022430 9925521 0.050123215839740984 0.2650798546205296 chr4 191154276 9497450 0.049684737368888364 0.3157211918137215 chr5 180915260 8929512 0.049357428444676256 0.26684537435112865 chr6 171115067 7668222 0.04481324838566086 0.3098030152183789 chr7 159138663 7043233 0.044258465335981864 0.4831962530122877 chr8 146364022 8010045 0.05472687133454149 0.6743641415480274 chr9 141213431 5777382 0.04091241151133847 0.3696627851707088 chr10 135534747 6912519 0.05100182169521444 0.37966792158160434 chr11 135006516 5750205 0.04259205533457363 0.4434302420150376 chr12 133851895 6566441 0.049057512409518 0.271740713974941 chr13 115169878 4270003 0.03707569265637322 0.22903469065503432 chr14 107349540 3852663 0.035888956766838495 0.2441096741309273 chr15 102531392 4194539 0.04090980253150177 0.2538390631809316 chr16 90354753 3955108 0.04377310400040604 0.2734839298559888 chr17 81195210 3604515 0.044393197579019744 0.2912657952362521 chr18 78077248 3713447 0.047561192218250316 0.6384830657175306 chr19 59128983 2959827 0.05005712680700089 0.47756883165998043 chr20 63025520 3135023 0.04974212033474694 0.27979318039042206 chr21 48129895 1800874 0.037416952602950825 0.26330150223375587 chr22 51304566 1575405 0.030706916027707944 0.20421805007975383 chrMT 16571 243731 14.708285559109287 12.990375471783283 chrX 155270560 7431904 0.04786421843265072 0.29756803952960337 chrY 59373566 401126 0.006755969483119811 0.17723099666224454