BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063582.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 = 3,096,989 number of mapped reads = 2,730,805 (88.18%) number of supplementary alignments = 30,855 (1%) number of secondary alignments = 0 number of mapped bases = 180,921,365 bp number of sequenced bases = 180,844,144 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 186,921 duplication rate = 5.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.9967 >>>>>>> ACTG content number of A's = 51,213,979 bp (28.32%) number of C's = 34,059,588 bp (18.83%) number of T's = 56,515,599 bp (31.25%) number of G's = 39,051,199 bp (21.59%) number of N's = 3,779 bp (0%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,437,949 number of insertions = 14,084 mapped reads with insertion percentage = 0.51% number of deletions = 46,817 mapped reads with deletion percentage = 1.7% homopolymer indels = 46.18% >>>>>>> Coverage mean coverageData = 0.0584X std coverageData = 0.6326X There is a 4.11% of reference with a coverageData >= 1X There is a 1.11% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 8644868 0.03468343615480902 1.2294427574763465 chr2 243199373 12068006 0.0496218631287343 0.6264137069008858 chr3 198022430 5251700 0.02652073303009159 0.2151656179417399 chr4 191154276 2652354 0.013875462560931674 0.1892684922141213 chr5 180915260 5659437 0.03128225335994321 0.24381435737104562 chr6 171115067 23548324 0.13761689378294198 0.6420781244154316 chr7 159138663 13907074 0.08738966218410418 1.2389221620947475 chr8 146364022 8560056 0.058484700563913174 0.8832829744761982 chr9 141213431 5848868 0.04141863814639558 0.3758010355827108 chr10 135534747 5578644 0.04116024948200184 0.32593117200167265 chr11 135006516 9906987 0.07338154700622006 0.4031380888616193 chr12 133851895 5352044 0.03998482053616051 0.26675172769075983 chr13 115169878 8671521 0.07529330716144372 0.36130943923994085 chr14 107349540 11357117 0.10579567457857761 0.434154473098954 chr15 102531392 2926243 0.028539971446013335 0.22748618769780002 chr16 90354753 8115981 0.08982350933990157 0.4693925761551893 chr17 81195210 8993373 0.1107623590110796 0.48563829964535843 chr18 78077248 5445455 0.06974445359549558 0.6942351709416896 chr19 59128983 6016432 0.10175098056396471 1.1077842659267698 chr20 63025520 3001707 0.04762685020290194 0.30118303351481346 chr21 48129895 3167076 0.06580267835614434 0.3512976766539558 chr22 51304566 1682105 0.03278665294625044 0.23301801734471478 chrMT 16571 33024 1.992879126184298 1.9503066330713623 chrX 155270560 13775865 0.08872168040097234 0.4589094517143343 chrY 59373566 757104 0.012751533232819467 0.27899051343886