BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708640.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 2,398,614 number of mapped reads = 2,313,984 (96.47%) number of supplementary alignments = 56 (0%) number of secondary alignments = 0 number of mapped bases = 115,406,730 bp number of sequenced bases = 115,395,324 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,951 duplication rate = 0.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1356 >>>>>>> ACTG content number of A's = 35,665,543 bp (30.91%) number of C's = 21,946,686 bp (19.02%) number of T's = 35,592,890 bp (30.84%) number of G's = 22,186,092 bp (19.23%) number of N's = 4,113 bp (0%) GC percentage = 38.24% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 190,340 number of insertions = 7,949 mapped reads with insertion percentage = 0.34% number of deletions = 6,776 mapped reads with deletion percentage = 0.29% homopolymer indels = 48.56% >>>>>>> Coverage mean coverageData = 0.0373X std coverageData = 0.2001X There is a 3.54% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 8424716 0.03380018058209773 0.1908464822530206 chr2 243199373 9132739 0.03755247757156019 0.20035786359318122 chr3 198022430 8102299 0.040916066932417706 0.20870330213474128 chr4 191154276 9580297 0.05011814122327036 0.23151365773368754 chr5 180915260 7462710 0.0412497541666745 0.20943037629043393 chr6 171115067 7828139 0.045747806649896 0.22105813071553074 chr7 159138663 6700739 0.042106291919770625 0.21275818053680182 chr8 146364022 4967073 0.033936434187357874 0.1894544177752368 chr9 141213431 4711852 0.03336688278609986 0.18885308867397138 chr10 135534747 5204466 0.03839949618233323 0.2029784371849984 chr11 135006516 5602790 0.04150014507447922 0.21215004446667887 chr12 133851895 7501606 0.05604407767256489 0.24621724635093512 chr13 115169878 4651087 0.0403845786829782 0.2080135986949724 chr14 107349540 3448248 0.03212168398672225 0.18648132966071232 chr15 102531392 4010773 0.03911751242000108 0.20512473578242757 chr16 90354753 2149594 0.023790602360453578 0.15971515686471247 chr17 81195210 1801859 0.022191690864522672 0.15311069209771644 chr18 78077248 4164965 0.05334415731456109 0.23969758178039574 chr19 59128983 837623 0.014166030895542378 0.12207135651948782 chr20 63025520 1908945 0.030288445061619484 0.178937558158039 chr21 48129895 1520457 0.03159069846298231 0.18439906604976175 chr22 51304566 813851 0.01586312999899463 0.12919595274910634 chrMT 16571 150 0.009051958240299317 0.09471019106894038 chrX 155270560 4469503 0.02878525716658715 0.17563865040267734 chrY 59373566 410249 0.006909623720428044 0.08565827977517662