BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085043.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 = 2,957,243 number of mapped reads = 2,635,906 (89.13%) number of supplementary alignments = 17,872 (0.6%) number of secondary alignments = 0 number of mapped bases = 174,193,654 bp number of sequenced bases = 174,135,638 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,373 duplication rate = 2.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0259 >>>>>>> ACTG content number of A's = 48,900,766 bp (28.08%) number of C's = 33,684,583 bp (19.34%) number of T's = 52,933,702 bp (30.4%) number of G's = 38,598,121 bp (22.17%) number of N's = 18,466 bp (0.01%) GC percentage = 41.51% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,591,116 number of insertions = 12,584 mapped reads with insertion percentage = 0.47% number of deletions = 34,087 mapped reads with deletion percentage = 1.28% homopolymer indels = 45.79% >>>>>>> Coverage mean coverageData = 0.0563X std coverageData = 0.4685X There is a 4.76% of reference with a coverageData >= 1X There is a 0.62% 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 0.01% 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 15502162 0.06219507874365537 0.8391851837905476 chr2 243199373 17269027 0.07100769540224103 0.6017639335585898 chr3 198022430 11506522 0.058107164930760624 0.27757291321044913 chr4 191154276 12086621 0.06322966586423628 0.2963204369505257 chr5 180915260 8821083 0.04875809260092266 0.25557815568005227 chr6 171115067 12072709 0.07055316175050792 0.4312309709889106 chr7 159138663 14365750 0.09027190331490971 0.5554834305703231 chr8 146364022 10273202 0.07018939394819308 0.7161557213369543 chr9 141213431 5368702 0.03801835251775732 0.4400778131108667 chr10 135534747 10363775 0.07646581581031762 0.4925793926646728 chr11 135006516 6975186 0.05166555072052967 0.4356504862381296 chr12 133851895 7418841 0.05542574499972525 0.27965230332874697 chr13 115169878 3431369 0.029793979637627123 0.19464822706946222 chr14 107349540 4239722 0.03949455209589161 0.2618065762068355 chr15 102531392 2977507 0.029039954904737857 0.21012851293508067 chr16 90354753 4246133 0.046994019229956836 0.2792219726430876 chr17 81195210 4263000 0.052503097165460866 0.3190155325827594 chr18 78077248 4559937 0.05840289094205779 0.7470913882733937 chr19 59128983 3049210 0.051568788186328186 0.5452836085980326 chr20 63025520 3943149 0.06256432315036829 0.2895819248070699 chr21 48129895 1924732 0.03999036357756442 0.24806436176121177 chr22 51304566 1069637 0.020848768119391167 0.16046962863146677 chrMT 16571 40122 2.4212177901152616 2.3018448044537543 chrX 155270560 8070703 0.05197832093862481 0.31775854184387703 chrY 59373566 354853 0.005976615923658687 0.11235020660824177