BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238489.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 = 1,484,539 number of mapped reads = 1,170,448 (78.84%) number of supplementary alignments = 8,605 (0.58%) number of secondary alignments = 0 number of mapped bases = 69,770,583 bp number of sequenced bases = 69,733,063 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 307,945 duplication rate = 17.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4314 >>>>>>> ACTG content number of A's = 16,760,492 bp (24.04%) number of C's = 11,861,264 bp (17.01%) number of T's = 24,144,905 bp (34.62%) number of G's = 16,962,539 bp (24.32%) number of N's = 3,863 bp (0.01%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 485,954 number of insertions = 4,501 mapped reads with insertion percentage = 0.38% number of deletions = 22,528 mapped reads with deletion percentage = 1.9% homopolymer indels = 40.28% >>>>>>> Coverage mean coverageData = 0.0225X std coverageData = 0.502X There is a 1.29% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% 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 7873434 0.03158842280276605 0.6305500840168847 chr2 243199373 5133417 0.021107854583161282 1.2318685523967754 chr3 198022430 3827090 0.019326548007718117 0.2554569794396535 chr4 191154276 7953347 0.0416069531188515 0.37530970688767973 chr5 180915260 3316430 0.018331400015675847 0.2388898859889591 chr6 171115067 3925951 0.022943339057337364 0.4606868639917631 chr7 159138663 4030771 0.025328672014795047 0.36206473035530135 chr8 146364022 3456475 0.02361560547987674 0.4302645895069407 chr9 141213431 2306801 0.016335563718439784 0.24288647534098012 chr10 135534747 2872685 0.021195192108190528 0.2788026085699367 chr11 135006516 2350762 0.017412211422447196 0.24267207590669065 chr12 133851895 2412493 0.018023599890012763 0.2415670363074494 chr13 115169878 1649246 0.014320115890024647 0.3320488633929061 chr14 107349540 1322092 0.01231576772476156 0.19255036399201242 chr15 102531392 1572019 0.01533207507804049 0.3047249532405762 chr16 90354753 1712377 0.018951709159118615 0.24867516487625083 chr17 81195210 1564032 0.019262614136966946 0.246814823977876 chr18 78077248 1944400 0.02490354168220683 0.916414919407355 chr19 59128983 1617409 0.027353912040056567 0.39649792020172103 chr20 63025520 1293920 0.020530096380006066 0.24764298432014795 chr21 48129895 758234 0.01575390929068098 0.21763745567284504 chr22 51304566 547049 0.010662774147626548 0.18097033327011103 chrMT 16571 43941 2.6516806469132823 2.9679970966357456 chrX 155270560 6048643 0.03895550450774442 0.3647032683658461 chrY 59373566 237565 0.004001191371931408 0.20111886968888726