BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084907.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 = 1,601,632 number of mapped reads = 1,420,226 (88.67%) number of supplementary alignments = 16,508 (1.03%) number of secondary alignments = 0 number of mapped bases = 97,088,595 bp number of sequenced bases = 97,052,918 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,820 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1383 >>>>>>> ACTG content number of A's = 27,604,183 bp (28.44%) number of C's = 18,364,736 bp (18.92%) number of T's = 29,356,431 bp (30.25%) number of G's = 21,712,665 bp (22.37%) number of N's = 14,903 bp (0.02%) GC percentage = 41.29% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 952,472 number of insertions = 9,159 mapped reads with insertion percentage = 0.64% number of deletions = 20,702 mapped reads with deletion percentage = 1.44% homopolymer indels = 44.12% >>>>>>> Coverage mean coverageData = 0.0314X std coverageData = 0.64X There is a 2.78% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 8108543 0.03253168625004148 1.5243082413049502 chr2 243199373 8568400 0.03523199872723356 0.7756418693523649 chr3 198022430 7094564 0.03582707272100438 0.2067257487699563 chr4 191154276 5474189 0.02863754405368363 0.19113745930068549 chr5 180915260 5071832 0.028034296277715875 0.213966234437131 chr6 171115067 5352367 0.031279343741249854 0.22471673083598015 chr7 159138663 5768916 0.03625087638193869 0.6923938678099286 chr8 146364022 5491524 0.03751963033647709 0.7424233675244498 chr9 141213431 6349311 0.044962514932450015 0.6632061117175106 chr10 135534747 3558931 0.02625843983757169 0.440763504854197 chr11 135006516 4111889 0.0304569669807641 0.4913356717430436 chr12 133851895 4113453 0.03073137664580692 0.2190957896216481 chr13 115169878 2543490 0.022084680857263738 0.15578863549011826 chr14 107349540 1972253 0.01837225385409197 0.23312238745969666 chr15 102531392 2371091 0.023125512623489983 0.16758799715912975 chr16 90354753 2028606 0.022451569315894208 0.286486071741236 chr17 81195210 2716229 0.03345306946062459 0.2640492270476919 chr18 78077248 3710442 0.04752270469369002 1.2915708110051831 chr19 59128983 2409698 0.04075324617032564 0.8755958807546839 chr20 63025520 1814302 0.028786783512456542 0.2295880695408586 chr21 48129895 955710 0.01985688936159117 0.21251002602267513 chr22 51304566 936210 0.0182480834162012 0.14113038529287344 chrMT 16571 50381 3.040311387363466 2.476486696962874 chrX 155270560 6193072 0.03988568083994802 0.3228137069411472 chrY 59373566 323192 0.005443365150073687 0.20620758639223277