BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083620.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 = 1,841,763 number of mapped reads = 1,642,344 (89.17%) number of supplementary alignments = 15,684 (0.85%) number of secondary alignments = 0 number of mapped bases = 108,239,302 bp number of sequenced bases = 108,200,994 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,181 duplication rate = 4.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1901 >>>>>>> ACTG content number of A's = 28,616,737 bp (26.45%) number of C's = 20,393,147 bp (18.85%) number of T's = 33,841,869 bp (31.28%) number of G's = 25,344,049 bp (23.42%) number of N's = 5,192 bp (0%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 755,171 number of insertions = 7,775 mapped reads with insertion percentage = 0.47% number of deletions = 23,782 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.54% >>>>>>> Coverage mean coverageData = 0.035X std coverageData = 0.2952X There is a 2.93% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.08% 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% 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 11650776 0.04674321754247505 0.5034244904930433 chr2 243199373 9676958 0.03979022593943941 0.45640010272661735 chr3 198022430 7823857 0.03950995349365221 0.23212171318271496 chr4 191154276 4388522 0.02295801115116044 0.1835156599379033 chr5 180915260 5452961 0.030140967655243676 0.2006956988211664 chr6 171115067 7355717 0.04298696268517371 0.27213706544646704 chr7 159138663 7908284 0.049694297104909066 0.4027580947449816 chr8 146364022 8144147 0.05564309376521506 0.3095026550915178 chr9 141213431 4073437 0.028845960126838075 0.22397505219776656 chr10 135534747 3926908 0.028973441032062428 0.23275052072556676 chr11 135006516 4597848 0.034056489540104866 0.2473426964148231 chr12 133851895 4120477 0.030783852555841665 0.20352805993444126 chr13 115169878 3642115 0.031623850465483695 0.20790848741898083 chr14 107349540 2713777 0.02527981955022816 0.1850129119674724 chr15 102531392 2582792 0.025190255877926636 0.19426228554609667 chr16 90354753 3278294 0.03628247426009786 0.22495482147105933 chr17 81195210 2084628 0.025674273149856992 0.19420760146000596 chr18 78077248 2365242 0.03029361383229081 0.329751632432144 chr19 59128983 3303895 0.055876066733635515 0.3820587630696951 chr20 63025520 1666535 0.02644222530809742 0.1937581696814864 chr21 48129895 1919332 0.0398781671973313 0.23521457056724768 chr22 51304566 680556 0.013265018166219358 0.13231537535657606 chrMT 16571 2899 0.17494417959085148 0.4392925022837028 chrX 155270560 4678323 0.030130135422967497 0.2116073343411166 chrY 59373566 201022 0.003385715454584621 0.07305436985805583