BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234103.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 = 5,284,526 number of mapped reads = 5,009,240 (94.79%) number of supplementary alignments = 35,052 (0.66%) number of secondary alignments = 0 number of mapped bases = 323,303,302 bp number of sequenced bases = 323,175,321 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 554,446 duplication rate = 9.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.271 >>>>>>> ACTG content number of A's = 83,447,968 bp (25.82%) number of C's = 58,885,939 bp (18.22%) number of T's = 104,464,273 bp (32.32%) number of G's = 76,346,328 bp (23.62%) number of N's = 30,813 bp (0.01%) GC percentage = 41.84% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,738,762 number of insertions = 20,254 mapped reads with insertion percentage = 0.4% number of deletions = 73,694 mapped reads with deletion percentage = 1.46% homopolymer indels = 44.48% >>>>>>> Coverage mean coverageData = 0.1044X std coverageData = 1.0035X There is a 7.89% of reference with a coverageData >= 1X There is a 1.72% of reference with a coverageData >= 2X There is a 0.42% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 24647194 0.09888518592697909 2.0280810744465616 chr2 243199373 37326798 0.1534822953675954 1.7279161650497352 chr3 198022430 41623766 0.21019722866747975 0.5824753780103457 chr4 191154276 5245569 0.0274415467431134 0.2916521096218653 chr5 180915260 20045823 0.11080227837054762 0.42403711495609836 chr6 171115067 35278070 0.2061657726493483 0.9634479948578398 chr7 159138663 19796006 0.1243946984775158 1.4011110467843262 chr8 146364022 4752822 0.03247261133613833 0.7952316599823056 chr9 141213431 8544292 0.06050622762646423 0.5586512813321204 chr10 135534747 10426178 0.07692623648753334 0.7453090130563991 chr11 135006516 13246379 0.09811659016517395 0.7530335965155256 chr12 133851895 14419712 0.10772885957273896 0.4164233550810511 chr13 115169878 11959082 0.10383862697154199 0.44893338196529015 chr14 107349540 14835765 0.1382005456194782 0.49451154527956803 chr15 102531392 7041430 0.06867584514994197 0.37377030080151796 chr16 90354753 10929454 0.12096158350407975 0.5249924795304176 chr17 81195210 5357270 0.06598012370434167 0.42048075486986924 chr18 78077248 9110690 0.11668815478742284 1.597449087326485 chr19 59128983 8053419 0.13620087123771435 1.251942793710253 chr20 63025520 6443820 0.10224144124475291 0.43387105612459087 chr21 48129895 5309769 0.11032164105074403 0.44190543628005935 chr22 51304566 2246057 0.043778890947055275 0.25389266770477503 chrMT 16571 419394 25.30891316154728 13.33948514744665 chrX 155270560 5586058 0.035976285523797946 0.3756446843724985 chrY 59373566 658485 0.011090541538300058 0.24004869325164202