BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081252.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 = 2,932,470 number of mapped reads = 2,408,032 (82.12%) number of supplementary alignments = 21,436 (0.73%) number of secondary alignments = 0 number of mapped bases = 161,783,997 bp number of sequenced bases = 161,715,055 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,550 duplication rate = 3.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8475 >>>>>>> ACTG content number of A's = 44,944,482 bp (27.79%) number of C's = 29,217,096 bp (18.07%) number of T's = 52,095,181 bp (32.21%) number of G's = 35,416,452 bp (21.9%) number of N's = 41,844 bp (0.03%) GC percentage = 39.97% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,372,351 number of insertions = 12,850 mapped reads with insertion percentage = 0.53% number of deletions = 41,253 mapped reads with deletion percentage = 1.69% homopolymer indels = 49.71% >>>>>>> Coverage mean coverageData = 0.0523X std coverageData = 0.4284X There is a 4.4% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.1% 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 16819747 0.06748126416904694 0.8121933586385702 chr2 243199373 10059824 0.041364514537625886 0.44377160553771666 chr3 198022430 11067249 0.055888865720918585 0.2820090162376196 chr4 191154276 8270714 0.043267219405544455 0.2575011897751497 chr5 180915260 10883570 0.06015838575474507 0.2813525916098244 chr6 171115067 11332788 0.06622904808259812 0.3570821516352167 chr7 159138663 10263143 0.0644918262257865 0.48106596171809607 chr8 146364022 8968246 0.06127356899224865 0.627365236125333 chr9 141213431 5448895 0.038586237593788084 0.35563804840666213 chr10 135534747 4987206 0.036796512410208725 0.5324382621257383 chr11 135006516 8697632 0.06442379418190453 0.4218210562385613 chr12 133851895 4015284 0.02999796155295373 0.203745989726566 chr13 115169878 5380114 0.046714593202920644 0.24436834833721327 chr14 107349540 6121036 0.05701967609735449 0.27932057416418027 chr15 102531392 5481964 0.053466200868510595 0.2624349758517547 chr16 90354753 4836734 0.05353048776526455 0.2968216056863729 chr17 81195210 2132316 0.02626159843665655 0.22697824824477908 chr18 78077248 5089719 0.06518824792595149 0.5744243864780664 chr19 59128983 3651302 0.06175147642908047 0.5940236289632437 chr20 63025520 3311049 0.05253505246763533 0.26727355666825614 chr21 48129895 2536694 0.05270516380723457 0.2798772955593797 chr22 51304566 1076817 0.02098871667679637 0.1622551462542541 chrMT 16571 44202 2.667431054251403 2.108318677678875 chrX 155270560 10851677 0.0698888250290332 0.3373981039084143 chrY 59373566 456075 0.0076814486770088895 0.16804231972871422