BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618574.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 = 66,468,992 number of mapped reads = 62,739,404 (94.39%) number of supplementary alignments = 66,177 (0.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 31,688,263 number of mapped paired reads (second in pair) = 31,051,141 number of mapped paired reads (both in pair) = 61,528,524 number of mapped paired reads (singletons) = 1,210,880 number of mapped bases = 6,002,615,866 bp number of sequenced bases = 5,998,826,790 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,869,303 duplication rate = 16.66% >>>>>>> Insert size mean insert size = 22,326.9242 std insert size = 1,486,796.7951 median insert size = 209 >>>>>>> Mapping quality mean mapping quality = 52.6446 >>>>>>> ACTG content number of A's = 1,607,461,619 bp (26.8%) number of C's = 1,365,302,059 bp (22.76%) number of T's = 1,612,546,384 bp (26.88%) number of G's = 1,413,246,622 bp (23.56%) number of N's = 270,106 bp (0%) GC percentage = 46.32% >>>>>>> Mismatches and indels general error rate = 0.0133 number of mismatches = 78,377,825 number of insertions = 1,048,565 mapped reads with insertion percentage = 1.65% number of deletions = 2,751,649 mapped reads with deletion percentage = 4.28% homopolymer indels = 52.32% >>>>>>> Coverage mean coverageData = 1.939X std coverageData = 8.0718X There is a 27.55% of reference with a coverageData >= 1X There is a 19.72% of reference with a coverageData >= 2X There is a 15.24% of reference with a coverageData >= 3X There is a 12.35% of reference with a coverageData >= 4X There is a 10.3% of reference with a coverageData >= 5X There is a 8.77% of reference with a coverageData >= 6X There is a 7.58% of reference with a coverageData >= 7X There is a 6.63% of reference with a coverageData >= 8X There is a 5.86% of reference with a coverageData >= 9X There is a 5.22% of reference with a coverageData >= 10X There is a 4.68% of reference with a coverageData >= 11X There is a 4.22% of reference with a coverageData >= 12X There is a 3.83% of reference with a coverageData >= 13X There is a 3.49% of reference with a coverageData >= 14X There is a 3.19% of reference with a coverageData >= 15X There is a 2.93% of reference with a coverageData >= 16X There is a 2.69% of reference with a coverageData >= 17X There is a 2.49% of reference with a coverageData >= 18X There is a 2.3% of reference with a coverageData >= 19X There is a 2.14% of reference with a coverageData >= 20X There is a 1.99% of reference with a coverageData >= 21X There is a 1.85% of reference with a coverageData >= 22X There is a 1.73% of reference with a coverageData >= 23X There is a 1.62% of reference with a coverageData >= 24X There is a 1.52% of reference with a coverageData >= 25X There is a 1.43% of reference with a coverageData >= 26X There is a 1.34% of reference with a coverageData >= 27X There is a 1.27% of reference with a coverageData >= 28X There is a 1.19% of reference with a coverageData >= 29X There is a 1.13% of reference with a coverageData >= 30X There is a 1.06% of reference with a coverageData >= 31X There is a 1.01% of reference with a coverageData >= 32X There is a 0.95% of reference with a coverageData >= 33X There is a 0.9% of reference with a coverageData >= 34X There is a 0.86% of reference with a coverageData >= 35X There is a 0.82% of reference with a coverageData >= 36X There is a 0.78% of reference with a coverageData >= 37X There is a 0.74% of reference with a coverageData >= 38X There is a 0.7% of reference with a coverageData >= 39X There is a 0.67% of reference with a coverageData >= 40X There is a 0.64% of reference with a coverageData >= 41X There is a 0.61% of reference with a coverageData >= 42X There is a 0.58% of reference with a coverageData >= 43X There is a 0.56% of reference with a coverageData >= 44X There is a 0.53% of reference with a coverageData >= 45X There is a 0.51% of reference with a coverageData >= 46X There is a 0.49% of reference with a coverageData >= 47X There is a 0.47% of reference with a coverageData >= 48X There is a 0.45% of reference with a coverageData >= 49X There is a 0.43% of reference with a coverageData >= 50X There is a 0.41% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 570721080 2.289747875893958 9.842213752482323 chr2 243199373 492915724 2.026796853625112 8.328166140783056 chr3 198022430 394557298 1.9924879115966811 7.09361476866858 chr4 191154276 279476882 1.4620488112962746 6.8143115076856855 chr5 180915260 345999628 1.9124955407299529 6.696122644630921 chr6 171115067 322108664 1.8824097120565075 6.957167888223679 chr7 159138663 303478037 1.9070038121408623 7.124605145153795 chr8 146364022 282608290 1.9308590057739736 7.146309077986449 chr9 141213431 278221171 1.9702174858990573 8.776027675664801 chr10 135534747 310630483 2.2918881679839633 8.325321283312821 chr11 135006516 330069302 2.444839788325476 9.261053289061653 chr12 133851895 280697993 2.0970789617883256 7.431724047373288 chr13 115169878 154608345 1.3424373428614729 5.545456486662257 chr14 107349540 198665572 1.8506420428070767 7.412265768608597 chr15 102531392 202311006 1.9731616049843546 7.607822108098994 chr16 90354753 230042772 2.5459952505210213 11.483666993883018 chr17 81195210 228720493 2.8169210104881803 9.929782177942727 chr18 78077248 161101156 2.0633559727924835 8.691245512042817 chr19 59128983 152678765 2.5821307462704035 9.898282115826175 chr20 63025520 201832821 3.202398345939867 10.116679234890142 chr21 48129895 86102127 1.7889531444022473 13.699025662082576 chr22 51304566 133866437 2.6092499642234572 9.904304072858594 chrMT 16571 1681 0.10144227867962102 0.46973938732073134 chrX 155270560 8379732 0.05396858232494299 1.528745563946014 chrY 59373566 52820407 0.8896283406659455 5.435747860274172