BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237281.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 = 2,559,406 number of mapped reads = 2,309,266 (90.23%) number of supplementary alignments = 10,580 (0.41%) number of secondary alignments = 0 number of mapped bases = 156,423,107 bp number of sequenced bases = 156,348,637 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,336 duplication rate = 3.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.427 >>>>>>> ACTG content number of A's = 44,088,501 bp (28.2%) number of C's = 28,355,928 bp (18.14%) number of T's = 50,071,619 bp (32.03%) number of G's = 33,829,974 bp (21.64%) number of N's = 2,615 bp (0%) GC percentage = 39.77% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,232,200 number of insertions = 12,612 mapped reads with insertion percentage = 0.54% number of deletions = 42,791 mapped reads with deletion percentage = 1.83% homopolymer indels = 46.98% >>>>>>> Coverage mean coverageData = 0.0505X std coverageData = 0.5275X There is a 4.13% of reference with a coverageData >= 1X There is a 0.65% 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 0.01% 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 9772162 0.03920616911923361 0.6905928415720144 chr2 243199373 12998595 0.05344830802668229 0.5756454716920766 chr3 198022430 11300666 0.057067605927267936 0.2779442283208761 chr4 191154276 7504870 0.03926080105056086 0.2917682619178371 chr5 180915260 7235830 0.039995686378252446 0.24030397717987953 chr6 171115067 13875945 0.08109131032862232 0.4571584097360985 chr7 159138663 12295293 0.07726150746911829 0.7322326378542166 chr8 146364022 8366032 0.057159074242985754 1.2696469877272076 chr9 141213431 7758796 0.05494375389831014 0.532069909217945 chr10 135534747 5408486 0.039904792827775745 0.43756872650391576 chr11 135006516 6107188 0.04523624622681175 0.40290517284105093 chr12 133851895 4943999 0.03693633922777111 0.24192250965653614 chr13 115169878 6031229 0.052368111391070504 0.26890844092612215 chr14 107349540 4801203 0.0447249517790202 0.27519172259936014 chr15 102531392 5192856 0.05064649858650119 0.27017519190238926 chr16 90354753 4092921 0.045298347503644885 0.30747780319002327 chr17 81195210 4106002 0.050569510196475875 0.32894474624592884 chr18 78077248 4028838 0.05160066604806563 1.0049334339172984 chr19 59128983 2674548 0.045232437026694675 0.46841112414919917 chr20 63025520 3322742 0.05272058048866554 0.28271567944249376 chr21 48129895 2988417 0.062090661116131665 0.33783365307947866 chr22 51304566 1907671 0.03718325967322285 0.2202501377062207 chrMT 16571 53332 3.2183935791442884 2.8325279736185367 chrX 155270560 9250760 0.05957832573026078 0.3384877784952413 chrY 59373566 404726 0.006816602526450912 0.19816911023453657