BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971277.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,953,542 number of mapped reads = 8,667,412 (72.51%) number of secondary alignments = 0 number of mapped bases = 342,624,177 bp number of sequenced bases = 342,591,442 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 466,240 duplication rate = 4.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3266 >>>>>>> ACTG content number of A's = 98,667,184 bp (28.8%) number of C's = 70,750,729 bp (20.65%) number of T's = 100,670,306 bp (29.38%) number of G's = 72,500,379 bp (21.16%) number of N's = 2,844 bp (0%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 935,413 number of insertions = 10,326 mapped reads with insertion percentage = 0.12% number of deletions = 25,643 mapped reads with deletion percentage = 0.3% homopolymer indels = 41.85% >>>>>>> Coverage mean coverageData = 0.1107X std coverageData = 0.7318X There is a 8.51% of reference with a coverageData >= 1X There is a 1.83% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.12% 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% 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 28700192 0.11514591973674561 1.1125293951626236 chr2 243199373 28891949 0.11879943868111864 0.5534110979299246 chr3 198022430 24416084 0.12329958782952012 0.4360212050540444 chr4 191154276 20893361 0.10930103912506775 0.42088442158145534 chr5 180915260 21462801 0.11863455299458985 0.4298743818021882 chr6 171115067 20617961 0.12049179164333904 0.5426096031689838 chr7 159138663 18216089 0.11446677166063661 0.8132068889411009 chr8 146364022 17129520 0.11703367921933712 2.0165008966794242 chr9 141213431 14257294 0.10096273349522965 0.5320624863081227 chr10 135534747 16468254 0.12150577150522146 0.5505963066070131 chr11 135006516 16126053 0.11944647916105026 0.6113533367472512 chr12 133851895 15898216 0.11877468002974481 0.43732527027745155 chr13 115169878 12883437 0.11186464050956102 0.41429407198083285 chr14 107349540 10426492 0.09712656430572501 0.42700412281029704 chr15 102531392 10960745 0.10690135758617224 0.4009852247179264 chr16 90354753 9391211 0.10393710002173322 0.41163150338097615 chr17 81195210 8919489 0.10985240385485794 0.4385973225543489 chr18 78077248 8313307 0.10647541009642143 0.8526233639135264 chr19 59128983 5896471 0.09972217854651753 0.9839317399585875 chr20 63025520 7606556 0.1206900950599059 0.4361485180097635 chr21 48129895 4269645 0.08871087294081983 0.40517357758506606 chr22 51304566 4021184 0.07837867686084704 0.3448311387930912 chrMT 16571 23734 1.4322611791684268 1.7976157495260479 chrX 155270560 15973018 0.10287216069807438 0.4511134620355171 chrY 59373566 861114 0.0145033229097272 0.21451835791721685