BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240018.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 = 1,660,984 number of mapped reads = 1,242,958 (74.83%) number of supplementary alignments = 5,776 (0.35%) number of secondary alignments = 0 number of mapped bases = 76,938,077 bp number of sequenced bases = 76,897,328 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 69,001 duplication rate = 4.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2027 >>>>>>> ACTG content number of A's = 20,917,557 bp (27.2%) number of C's = 13,277,163 bp (17.27%) number of T's = 25,070,906 bp (32.6%) number of G's = 17,580,648 bp (22.86%) number of N's = 51,054 bp (0.07%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 740,380 number of insertions = 5,581 mapped reads with insertion percentage = 0.44% number of deletions = 23,881 mapped reads with deletion percentage = 1.89% homopolymer indels = 48.78% >>>>>>> Coverage mean coverageData = 0.0249X std coverageData = 0.2466X There is a 2.08% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 5125155 0.02056225569042815 0.336515028643879 chr2 243199373 8237207 0.033870181893931116 0.30402561747131784 chr3 198022430 5222117 0.02637134086274974 0.18812172152341747 chr4 191154276 4858443 0.025416344858537197 0.18905127077965606 chr5 180915260 4094305 0.022631064952729804 0.18807498894239083 chr6 171115067 4169696 0.02436778989193278 0.22593209987945048 chr7 159138663 4655507 0.029254405637428284 0.38486931679904235 chr8 146364022 4773932 0.032616840769789726 0.3455639156067062 chr9 141213431 2707369 0.019172177751279197 0.21387547045947455 chr10 135534747 3787814 0.027947180216450325 0.23103508460825573 chr11 135006516 3707066 0.027458422821606626 0.2491386361221362 chr12 133851895 3826980 0.02859115293063277 0.19809446636443684 chr13 115169878 1504472 0.013063068452673016 0.13127753229721156 chr14 107349540 3074285 0.028638082659692813 0.19998775389988055 chr15 102531392 1726983 0.016843456099766986 0.1652652828483591 chr16 90354753 2507300 0.02774950865064066 0.19749660930660176 chr17 81195210 2044419 0.025179059208049342 0.1976775390597664 chr18 78077248 1736602 0.022242100541248585 0.32969189095492546 chr19 59128983 1457930 0.024656774495850877 0.2658606029942807 chr20 63025520 1661374 0.02636033784409871 0.19095398669616423 chr21 48129895 1473859 0.030622526810000314 0.21049632817706546 chr22 51304566 725099 0.014133225491080073 0.13470659854772882 chrMT 16571 20162 1.2167038802727657 1.4073392257359716 chrX 155270560 3688188 0.02375329875798735 0.19650088735732357 chrY 59373566 151813 0.0025569122797845763 0.06267012046308892