BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081952.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 = 2,649,298 number of mapped reads = 2,465,007 (93.04%) number of supplementary alignments = 17,094 (0.65%) number of secondary alignments = 0 number of mapped bases = 169,580,322 bp number of sequenced bases = 169,518,322 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,705 duplication rate = 3.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9134 >>>>>>> ACTG content number of A's = 48,513,542 bp (28.62%) number of C's = 31,422,637 bp (18.54%) number of T's = 53,643,050 bp (31.64%) number of G's = 35,916,910 bp (21.19%) number of N's = 22,183 bp (0.01%) GC percentage = 39.72% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,246,698 number of insertions = 11,924 mapped reads with insertion percentage = 0.48% number of deletions = 35,130 mapped reads with deletion percentage = 1.41% homopolymer indels = 48.75% >>>>>>> Coverage mean coverageData = 0.0548X std coverageData = 0.4371X There is a 4.65% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 15440360 0.061947127505852836 0.7387298837431373 chr2 243199373 14876881 0.061171543398674796 0.5396936501957252 chr3 198022430 10963247 0.05536366259115192 0.2664366834337589 chr4 191154276 8844601 0.0462694384090053 0.255615892259379 chr5 180915260 8531253 0.04715607185375076 0.24798570719249657 chr6 171115067 14889531 0.08701472793158536 0.41055157583572705 chr7 159138663 11164364 0.07015494405655526 0.5612883998856548 chr8 146364022 9695979 0.0662456447117858 0.7147338153491701 chr9 141213431 8279487 0.058631016478878695 0.4556793060964173 chr10 135534747 6732014 0.049670022994177276 0.41128902044645416 chr11 135006516 7605029 0.05633082924678984 0.3362051800309335 chr12 133851895 7180833 0.053647600581224496 0.2705335531657107 chr13 115169878 4557585 0.03957271709535023 0.22373276923411503 chr14 107349540 4280524 0.03987463756248979 0.2521593570556607 chr15 102531392 3872923 0.03777304613205681 0.22027059143985098 chr16 90354753 3563198 0.039435645405394446 0.26753240820698926 chr17 81195210 4371882 0.05384408760073408 0.28855775496612335 chr18 78077248 4883423 0.06254604414335915 0.7210702836576572 chr19 59128983 3370813 0.057007795990673474 0.5453633989474943 chr20 63025520 4305531 0.06831408927685166 0.30092374863065413 chr21 48129895 1992281 0.041393836408743466 0.2523589290594637 chr22 51304566 1299909 0.025337101574935846 0.1771135635908941 chrMT 16571 74898 4.5198237885462555 3.1603827692393955 chrX 155270560 8454382 0.05444935601443055 0.30321179767157563 chrY 59373566 349394 0.0058846726504518864 0.13753042068415855