BamQC report ----------------------------------- >>>>>>> Input bam file = SRR23117299.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP418207/SRP418207.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 = 1,765,350 number of mapped reads = 1,684,715 (95.43%) number of supplementary alignments = 9,860 (0.56%) number of secondary alignments = 0 number of mapped bases = 394,578,279 bp number of sequenced bases = 393,805,738 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 785,321 duplication rate = 33.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 53.7467 >>>>>>> ACTG content number of A's = 116,582,193 bp (29.6%) number of C's = 80,512,155 bp (20.44%) number of T's = 115,924,566 bp (29.44%) number of G's = 80,786,824 bp (20.51%) number of N's = 0 bp (0%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,963,582 number of insertions = 1,285,915 mapped reads with insertion percentage = 35% number of deletions = 615,858 mapped reads with deletion percentage = 25.07% homopolymer indels = 33.13% >>>>>>> Coverage mean coverageData = 0.1275X std coverageData = 1.7581X There is a 5.93% of reference with a coverageData >= 1X There is a 2.53% of reference with a coverageData >= 2X There is a 1.42% of reference with a coverageData >= 3X There is a 0.88% of reference with a coverageData >= 4X There is a 0.57% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 27824125 0.11163111605647714 5.196721706753454 chr2 243199373 35523679 0.1460681356279648 0.7856561062523533 chr3 198022430 29257037 0.14774607603795187 0.7573071577442207 chr4 191154276 22437082 0.11737682498925632 0.7690887963790334 chr5 180915260 29668968 0.16399372833446996 0.8158365297426668 chr6 171115067 32382376 0.18924327686468428 0.9073820720631796 chr7 159138663 17517665 0.11007799531406143 2.696029083777533 chr8 146364022 13202683 0.09020442879056713 0.5502187286195679 chr9 141213431 17737583 0.12560832828996274 0.7296615254500161 chr10 135534747 28233852 0.2083144922239018 1.2424061448407666 chr11 135006516 17676846 0.13093328028700482 0.7107172014660739 chr12 133851895 20114699 0.15027578802675898 0.7765795949698895 chr13 115169878 10450613 0.09074085326373273 0.5697963007114852 chr14 107349540 14597052 0.13597684722263365 0.7613236193049403 chr15 102531392 6422747 0.06264176146169946 0.44090226364248275 chr16 90354753 5411303 0.05988952235860796 0.7672715436824428 chr17 81195210 9202327 0.11333583594401689 0.699373162985921 chr18 78077248 10269983 0.13153618068095843 0.7878038714031237 chr19 59128983 5173936 0.08750253661558834 1.1343280987365905 chr20 63025520 8511978 0.13505605348436633 0.834219812610321 chr21 48129895 5282397 0.10975293006560684 0.8770502142495888 chr22 51304566 4726108 0.09211866249877253 0.6668139281932354 chrMT 16571 217406 13.119666887936758 30.813133031568153 chrX 155270560 22221924 0.14311743320820122 0.7395563465506911 chrY 59373566 513910 0.008655535360635068 0.5291817568673202