BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080710.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,158,424 number of mapped reads = 1,966,346 (91.1%) number of supplementary alignments = 12,309 (0.57%) number of secondary alignments = 0 number of mapped bases = 133,954,982 bp number of sequenced bases = 133,905,053 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,619 duplication rate = 4.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6423 >>>>>>> ACTG content number of A's = 37,687,384 bp (28.14%) number of C's = 24,743,641 bp (18.48%) number of T's = 42,629,069 bp (31.84%) number of G's = 28,842,865 bp (21.54%) number of N's = 2,094 bp (0%) GC percentage = 40.02% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,054,127 number of insertions = 9,533 mapped reads with insertion percentage = 0.48% number of deletions = 28,027 mapped reads with deletion percentage = 1.41% homopolymer indels = 48.92% >>>>>>> Coverage mean coverageData = 0.0433X std coverageData = 0.3405X There is a 3.53% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 16659113 0.06683679636649732 0.46258591026641394 chr2 243199373 8938445 0.0367535692618747 0.34859753982526 chr3 198022430 8167949 0.04124759503254252 0.23777071395263136 chr4 191154276 5810162 0.03039514533276776 0.2091500227292785 chr5 180915260 6037445 0.03337167356695063 0.21295336731009626 chr6 171115067 7914622 0.04625321509531361 0.31677418156139847 chr7 159138663 8311208 0.05222620225230873 0.7659485054043016 chr8 146364022 15909681 0.10869939745164969 0.502763454286958 chr9 141213431 4103749 0.029060613929846376 0.2470133511748133 chr10 135534747 6325415 0.04667006166322796 0.30108042993600975 chr11 135006516 5608406 0.0415417430666828 0.278932663368593 chr12 133851895 4435614 0.03313822340729655 0.2147443777222858 chr13 115169878 2931722 0.02545563172342685 0.1873451971022796 chr14 107349540 2656733 0.024748433947644304 0.19307637289219487 chr15 102531392 2337033 0.02279334118471736 0.1778648717141776 chr16 90354753 3094856 0.034252276689860466 0.2289346655879676 chr17 81195210 2254427 0.027765517202307872 0.21445523725859875 chr18 78077248 4376189 0.05604947807586661 0.40088183439463476 chr19 59128983 2124347 0.035927338713063944 0.2981776715378399 chr20 63025520 3438706 0.05456053357433624 0.2780173533389104 chr21 48129895 2016187 0.041890533939456964 0.24786117134357163 chr22 51304566 1325439 0.025834718102868272 0.18690775121058437 chrMT 16571 9776 0.5899462917144409 0.8798101091117649 chrX 155270560 8880190 0.057191717476899676 0.30113897910785387 chrY 59373566 287568 0.004843367501288368 0.10055531930067019