BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975304.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 3,671,970 number of mapped reads = 3,633,824 (98.96%) number of supplementary alignments = 13,973 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,816,148 number of mapped paired reads (second in pair) = 1,817,676 number of mapped paired reads (both in pair) = 3,622,794 number of mapped paired reads (singletons) = 11,030 number of mapped bases = 330,792,444 bp number of sequenced bases = 330,613,382 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,250 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 41,973.9896 std insert size = 1,965,302.7375 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 52.7978 >>>>>>> ACTG content number of A's = 96,122,664 bp (29.07%) number of C's = 66,388,573 bp (20.08%) number of T's = 97,276,444 bp (29.42%) number of G's = 70,818,802 bp (21.42%) number of N's = 6,899 bp (0%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 2,469,693 number of insertions = 48,367 mapped reads with insertion percentage = 1.3% number of deletions = 105,487 mapped reads with deletion percentage = 2.84% homopolymer indels = 46.26% >>>>>>> Coverage mean coverageData = 0.1069X std coverageData = 0.8905X There is a 7.41% of reference with a coverageData >= 1X There is a 2.19% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.05% 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 0.01% 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% 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 31656492 0.1270066725330245 0.9088528606192715 chr2 243199373 28624785 0.11770089966473721 1.1481537280793919 chr3 198022430 18230856 0.0920646009646483 0.39377250583169604 chr4 191154276 21131007 0.11054425484052473 0.7032236800669682 chr5 180915260 20860070 0.1153029877081679 0.44088816329995906 chr6 171115067 24542823 0.14342876656209355 0.8401612883378609 chr7 159138663 19784174 0.12432034822361175 1.0126628201414822 chr8 146364022 17712768 0.12101859294355823 0.5341032214787277 chr9 141213431 14395263 0.10193975812399884 1.3666414807469074 chr10 135534747 17731740 0.13082800088157467 1.8769650891135543 chr11 135006516 12444092 0.09217401032702748 0.8290567459329513 chr12 133851895 14914307 0.11142395107667322 0.5959107953299416 chr13 115169878 10993461 0.09545430793978961 0.4008439891802083 chr14 107349540 10058689 0.09370034561862119 0.4316768265342564 chr15 102531392 9922968 0.0967798037892629 0.40281147005523676 chr16 90354753 10922507 0.12088469767605917 1.3254719176755814 chr17 81195210 7323756 0.09019936028246 0.9320505044706788 chr18 78077248 8673523 0.11108899483752296 1.3891245221917359 chr19 59128983 4454617 0.07533728425533719 0.5983958960447716 chr20 63025520 7330518 0.11631031366341761 0.46711403533379925 chr21 48129895 4160352 0.0864400805362239 0.47681277859026255 chr22 51304566 3606489 0.07029567309856982 0.3582305577186383 chrMT 16571 94856 5.724217005612214 5.3659249332116445 chrX 155270560 10452411 0.06731740389163278 0.4709332392638931 chrY 59373566 769920 0.012967386867078188 0.7803184623507012