BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230364.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 = 1,491,366 number of mapped reads = 1,289,327 (86.45%) number of supplementary alignments = 14,456 (0.97%) number of secondary alignments = 0 number of mapped bases = 88,125,810 bp number of sequenced bases = 88,082,928 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,646 duplication rate = 6.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2105 >>>>>>> ACTG content number of A's = 25,997,250 bp (29.51%) number of C's = 16,301,262 bp (18.51%) number of T's = 28,049,056 bp (31.84%) number of G's = 17,695,124 bp (20.09%) number of N's = 40,236 bp (0.05%) GC percentage = 38.6% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 796,835 number of insertions = 8,241 mapped reads with insertion percentage = 0.63% number of deletions = 25,939 mapped reads with deletion percentage = 1.99% homopolymer indels = 45.7% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.4372X There is a 1.52% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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% 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 2087764 0.008376163684663398 0.27819909268348475 chr2 243199373 2124792 0.008736831735170633 0.2940309445497087 chr3 198022430 3647686 0.018420569831407482 0.2282043229678719 chr4 191154276 10406116 0.054438311387813264 0.4057975970315616 chr5 180915260 1974042 0.010911417864916426 0.17399023991237805 chr6 171115067 10790649 0.06306077652413858 0.46187158013668983 chr7 159138663 1247691 0.00784027574744674 0.21865904641777717 chr8 146364022 13922005 0.09511903820188816 1.4089067820638346 chr9 141213431 1110765 0.007865859445055195 0.2787294345128306 chr10 135534747 1212877 0.008948826974974912 0.18923636278324804 chr11 135006516 7155963 0.053004574979181006 0.45388800282925673 chr12 133851895 3204993 0.023944322939918033 0.2604345563058842 chr13 115169878 775080 0.006729884701275797 0.13378669282696998 chr14 107349540 847922 0.007898701755033138 0.16142102553922766 chr15 102531392 2828463 0.027586312297408388 0.2757950144685199 chr16 90354753 925583 0.010243877264541911 0.2073695407607164 chr17 81195210 6448848 0.07942399557806427 0.5175457177913142 chr18 78077248 6186568 0.07923650177834136 0.7257492288088042 chr19 59128983 1569343 0.026541011199194817 0.2967788191533014 chr20 63025520 2797260 0.04438297375412373 0.3483081977126196 chr21 48129895 2962142 0.06154474261786775 0.4228145239677739 chr22 51304566 1004288 0.019575021841135933 0.22222168878110107 chrMT 16571 3537 0.21344517530625792 0.6633354795569 chrX 155270560 2491627 0.01604700208461926 0.24038752574506123 chrY 59373566 399806 0.006733737367231741 0.1896239884792293