BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818739.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,180,489 number of mapped reads = 2,126,632 (97.53%) number of supplementary alignments = 19,237 (0.88%) number of secondary alignments = 0 number of mapped bases = 144,293,873 bp number of sequenced bases = 144,236,284 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,189,306 duplication rate = 46.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8252 >>>>>>> ACTG content number of A's = 40,544,083 bp (28.11%) number of C's = 31,415,888 bp (21.78%) number of T's = 41,329,721 bp (28.65%) number of G's = 30,937,644 bp (21.45%) number of N's = 8,948 bp (0.01%) GC percentage = 43.23% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 719,948 number of insertions = 17,321 mapped reads with insertion percentage = 0.81% number of deletions = 36,604 mapped reads with deletion percentage = 1.71% homopolymer indels = 39.24% >>>>>>> Coverage mean coverageData = 0.0466X std coverageData = 0.5975X There is a 1.7% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% 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 11952738 0.04795469697144707 0.7962170411145506 chr2 243199373 12842011 0.052804457682545096 0.9202848187200033 chr3 198022430 9826754 0.04962444910912365 0.48433170962990807 chr4 191154276 9854606 0.051553154897774824 0.5279251776302992 chr5 180915260 9122198 0.05042249061798325 0.49441429235042966 chr6 171115067 8332187 0.048693473614453836 0.5075767925588409 chr7 159138663 7952603 0.04997279008181689 0.5442963976404294 chr8 146364022 7345881 0.05018911683091081 0.5520911521902735 chr9 141213431 6162854 0.04364212353143661 0.5100688095933686 chr10 135534747 6861570 0.05062591071203313 0.5929996123118693 chr11 135006516 6864480 0.05084554585498673 0.5272370482081753 chr12 133851895 6535575 0.048826914254744024 0.501647443765987 chr13 115169878 4680885 0.04064330952925035 0.4400047566661701 chr14 107349540 4432354 0.04128898922156536 0.48405372814085845 chr15 102531392 4068771 0.039683173325102225 0.43456296213699314 chr16 90354753 4220642 0.046711897934135244 0.6557320317104706 chr17 81195210 3797107 0.04676516016154155 0.48882908073630926 chr18 78077248 3913452 0.050122821951921255 0.6580587359726957 chr19 59128983 2769177 0.04683281970197255 0.6819990711052784 chr20 63025520 3080681 0.04887989817458071 0.5180264193644076 chr21 48129895 2019475 0.04195884906875446 0.48886949674430574 chr22 51304566 1704455 0.03322228668691984 0.4362904222410898 chrMT 16571 91118 5.4986422062639555 7.011472328219506 chrX 155270560 4572781 0.02945040579489119 0.3903295259776796 chrY 59373566 1289518 0.021718722436176396 0.9716170647538636