BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472585.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 8,858,632 number of mapped reads = 8,009,113 (90.41%) number of supplementary alignments = 201,498 (2.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,041,888 number of mapped paired reads (second in pair) = 3,967,225 number of mapped paired reads (both in pair) = 7,818,342 number of mapped paired reads (singletons) = 190,771 number of mapped bases = 647,155,318 bp number of sequenced bases = 646,879,322 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,339,017 duplication rate = 14.38% >>>>>>> Insert size mean insert size = 163,932.626 std insert size = 3,860,462.8594 median insert size = 130 >>>>>>> Mapping quality mean mapping quality = 50.6813 >>>>>>> ACTG content number of A's = 169,822,348 bp (26.25%) number of C's = 126,313,315 bp (19.53%) number of T's = 195,486,909 bp (30.22%) number of G's = 154,826,091 bp (23.93%) number of N's = 430,659 bp (0.07%) GC percentage = 43.46% >>>>>>> Mismatches and indels general error rate = 0.0122 number of mismatches = 7,764,589 number of insertions = 60,813 mapped reads with insertion percentage = 0.75% number of deletions = 148,016 mapped reads with deletion percentage = 1.81% homopolymer indels = 43.37% >>>>>>> Coverage mean coverageData = 0.2091X std coverageData = 2.2744X There is a 11.4% of reference with a coverageData >= 1X There is a 5.18% of reference with a coverageData >= 2X There is a 1.86% of reference with a coverageData >= 3X There is a 0.89% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 43354085 0.1739377211020068 3.402139071464141 chr2 243199373 62956361 0.25886728334616227 2.9697870739262817 chr3 198022430 35397721 0.17875611868817082 0.6441901670044794 chr4 191154276 34515955 0.1805659581478575 1.1376882748017219 chr5 180915260 32405723 0.17912100394405647 0.6779280017362859 chr6 171115067 44399923 0.25947407074328527 1.1749484927589284 chr7 159138663 55531085 0.34894779152442673 3.9021656257516724 chr8 146364022 34785291 0.23766285269203657 1.839505057522829 chr9 141213431 21971168 0.15558837317676957 2.053392401493267 chr10 135534747 25065514 0.18493791853981179 2.0720431124853187 chr11 135006516 23072132 0.17089643288032114 1.2219011106632762 chr12 133851895 34528404 0.25795976963942124 0.8061685057402057 chr13 115169878 31055972 0.26965359813961076 0.823153583492775 chr14 107349540 16632327 0.15493617392305548 6.127650472377778 chr15 102531392 15088697 0.14716172974614447 0.5920874628880575 chr16 90354753 23621537 0.2614310394938493 1.222979938050861 chr17 81195210 22739010 0.2800535893681413 1.7055988371498114 chr18 78077248 15416203 0.19744808372344272 3.2044448160978645 chr19 59128983 11302790 0.19115481827245362 2.124945729081257 chr20 63025520 20488082 0.325075969226434 1.360818605446448 chr21 48129895 9917182 0.20605035602093044 0.8708753045122912 chr22 51304566 5728451 0.11165577348417682 0.5171839645760665 chrMT 16571 238826 14.412286524651499 9.008525903299095 chrX 155270560 25484594 0.16413023821128744 0.9066230124100654 chrY 59373566 1458285 0.024561182665026386 0.9556300580253079