BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630584.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 34,132,770 number of mapped reads = 33,809,245 (99.05%) number of supplementary alignments = 72,258 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,961,770 number of mapped paired reads (second in pair) = 16,847,475 number of mapped paired reads (both in pair) = 33,628,928 number of mapped paired reads (singletons) = 180,317 number of mapped bases = 3,274,641,364 bp number of sequenced bases = 3,272,302,204 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,479,497 duplication rate = 8.21% >>>>>>> Insert size mean insert size = 33,040.3856 std insert size = 1,790,946.4175 median insert size = 231 >>>>>>> Mapping quality mean mapping quality = 54.0611 >>>>>>> ACTG content number of A's = 958,520,153 bp (29.29%) number of C's = 645,940,078 bp (19.74%) number of T's = 971,724,432 bp (29.7%) number of G's = 695,745,850 bp (21.26%) number of N's = 371,691 bp (0.01%) GC percentage = 41% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 28,616,100 number of insertions = 592,920 mapped reads with insertion percentage = 1.72% number of deletions = 1,732,409 mapped reads with deletion percentage = 4.99% homopolymer indels = 54.23% >>>>>>> Coverage mean coverageData = 1.0578X std coverageData = 4.2684X There is a 22.47% of reference with a coverageData >= 1X There is a 15.04% of reference with a coverageData >= 2X There is a 11.01% of reference with a coverageData >= 3X There is a 8.5% of reference with a coverageData >= 4X There is a 6.77% of reference with a coverageData >= 5X There is a 5.52% of reference with a coverageData >= 6X There is a 4.57% of reference with a coverageData >= 7X There is a 3.83% of reference with a coverageData >= 8X There is a 3.24% of reference with a coverageData >= 9X There is a 2.77% of reference with a coverageData >= 10X There is a 2.38% of reference with a coverageData >= 11X There is a 2.06% of reference with a coverageData >= 12X There is a 1.79% of reference with a coverageData >= 13X There is a 1.56% of reference with a coverageData >= 14X There is a 1.37% of reference with a coverageData >= 15X There is a 1.21% of reference with a coverageData >= 16X There is a 1.07% of reference with a coverageData >= 17X There is a 0.95% of reference with a coverageData >= 18X There is a 0.84% of reference with a coverageData >= 19X There is a 0.75% of reference with a coverageData >= 20X There is a 0.67% of reference with a coverageData >= 21X There is a 0.6% of reference with a coverageData >= 22X There is a 0.54% of reference with a coverageData >= 23X There is a 0.48% of reference with a coverageData >= 24X There is a 0.43% of reference with a coverageData >= 25X There is a 0.39% of reference with a coverageData >= 26X There is a 0.35% of reference with a coverageData >= 27X There is a 0.32% of reference with a coverageData >= 28X There is a 0.29% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 292211946 1.1723619577260753 5.038380109640764 chr2 243199373 265243635 1.090642758359414 5.109476022280599 chr3 198022430 227597611 1.149352681915882 3.6463818013481855 chr4 191154276 188229186 0.9846977527199026 4.081549037531076 chr5 180915260 205296373 1.1347653757897482 3.6556404598642724 chr6 171115067 229099210 1.33886053412234 4.862179678790338 chr7 159138663 179096152 1.1254094298881976 3.8227903335175966 chr8 146364022 180156736 1.230881288572406 3.919841320561559 chr9 141213431 153861036 1.0895637540313003 5.535725851258853 chr10 135534747 164427253 1.2131741611617868 4.250548809509923 chr11 135006516 148531397 1.1001794683746968 5.361437995609553 chr12 133851895 139640620 1.043247239794401 3.599086892179552 chr13 115169878 101398867 0.8804287089719761 3.1699950872018796 chr14 107349540 91309412 0.8505803750998839 3.2412984961829996 chr15 102531392 97970451 0.9555166382604071 3.396027908499007 chr16 90354753 94245214 1.0430576242071072 4.843382304594585 chr17 81195210 76501106 0.9421874270662025 3.7871417210812455 chr18 78077248 88454873 1.1329148409534107 5.292097681829343 chr19 59128983 47218661 0.7985704912259357 3.4875499438970854 chr20 63025520 63399411 1.005932374695203 3.7316693157680887 chr21 48129895 39098861 0.8123612361921837 3.9389495658153058 chr22 51304566 31669335 0.6172810232913772 2.6873440888509226 chrMT 16571 890 0.05370828555910929 0.3061641224613629 chrX 155270560 165847999 1.068122630587537 3.918167829976345 chrY 59373566 4135129 0.06964595995463706 2.3491381766841912