BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081940.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 = 2,645,729 number of mapped reads = 2,406,297 (90.95%) number of supplementary alignments = 13,889 (0.52%) number of secondary alignments = 0 number of mapped bases = 161,952,989 bp number of sequenced bases = 161,888,741 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 126,836 duplication rate = 3.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4667 >>>>>>> ACTG content number of A's = 44,891,910 bp (27.73%) number of C's = 29,842,477 bp (18.43%) number of T's = 51,113,496 bp (31.57%) number of G's = 36,020,501 bp (22.25%) number of N's = 20,357 bp (0.01%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,283,116 number of insertions = 11,614 mapped reads with insertion percentage = 0.48% number of deletions = 36,855 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.04% >>>>>>> Coverage mean coverageData = 0.0523X std coverageData = 0.5074X There is a 4.46% of reference with a coverageData >= 1X There is a 0.55% 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 0.01% 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 15165738 0.0608453368707956 0.9230169172505563 chr2 243199373 13646729 0.05611333956851936 0.7122050268360974 chr3 198022430 10068023 0.0508428413892305 0.25471212002245724 chr4 191154276 8378325 0.04383017306921243 0.2570757216386637 chr5 180915260 8002081 0.0442311002399687 0.23912796352020838 chr6 171115067 13956024 0.08155929366523873 0.446544763936186 chr7 159138663 10630738 0.06680173001076425 0.7212563608381631 chr8 146364022 8712916 0.05952908290536044 0.6116675519758564 chr9 141213431 7967573 0.05642220391911588 0.5527804543229494 chr10 135534747 6598406 0.04868423888377495 0.48675340520213806 chr11 135006516 7518175 0.0556874973353138 0.37411703759244475 chr12 133851895 6901987 0.05156435775526376 0.27267709611980834 chr13 115169878 4265320 0.03703503098266719 0.2168335749655257 chr14 107349540 4135616 0.03852476685042153 0.2667711317987653 chr15 102531392 3783406 0.036899976935844195 0.2221055323939293 chr16 90354753 3591236 0.03974595558907676 0.27623252959873484 chr17 81195210 4567422 0.056252357743763456 0.30672360118635483 chr18 78077248 4813881 0.06165536213571462 0.8894678084380221 chr19 59128983 3672778 0.06211468240541191 0.6617956885283403 chr20 63025520 4122192 0.06540512478119974 0.2970261101114056 chr21 48129895 1712438 0.03557950832845158 0.24195889545140412 chr22 51304566 1409836 0.027479737378540536 0.1836254432473297 chrMT 16571 132033 7.967714682276266 4.826014610887258 chrX 155270560 7843130 0.05051266640630394 0.3195925822005212 chrY 59373566 356986 0.006012541001832364 0.15484914461633803