BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080951.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 = 4,099,259 number of mapped reads = 3,734,923 (91.11%) number of supplementary alignments = 47,378 (1.16%) number of secondary alignments = 0 number of mapped bases = 258,936,323 bp number of sequenced bases = 258,841,661 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 184,472 duplication rate = 3.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6822 >>>>>>> ACTG content number of A's = 75,357,176 bp (29.11%) number of C's = 46,260,139 bp (17.87%) number of T's = 82,317,436 bp (31.8%) number of G's = 53,634,835 bp (20.72%) number of N's = 1,272,075 bp (0.49%) GC percentage = 38.59% >>>>>>> Mismatches and indels general error rate = 0.0115 number of mismatches = 2,938,824 number of insertions = 19,391 mapped reads with insertion percentage = 0.52% number of deletions = 57,223 mapped reads with deletion percentage = 1.52% homopolymer indels = 49.73% >>>>>>> Coverage mean coverageData = 0.0836X std coverageData = 0.6157X There is a 5.85% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 21545092 0.08643947169945065 0.9089523764361731 chr2 243199373 17841666 0.07336230262402856 0.5303598269533678 chr3 198022430 23076556 0.11653506120493522 0.4607980333191805 chr4 191154276 17051729 0.08920401550420981 0.41694655702881006 chr5 180915260 15420389 0.08523542458496867 0.3915509168298552 chr6 171115067 22348023 0.1306023098480276 0.6446921015866405 chr7 159138663 12849084 0.08074143490824728 0.5732590047557894 chr8 146364022 20492199 0.14000844415166455 1.4221183147067056 chr9 141213431 13480475 0.09546170576366776 0.6540058098020761 chr10 135534747 11118139 0.08203165052575041 0.4702969527329139 chr11 135006516 11587551 0.08582956840394282 0.4753983099415706 chr12 133851895 10430929 0.07792888550438527 0.38714653234570656 chr13 115169878 7176059 0.06230847097016114 0.32975373542283387 chr14 107349540 7444686 0.06934995715864269 0.4091772334949865 chr15 102531392 6608270 0.06445118778841899 0.33685816852759143 chr16 90354753 5735434 0.0634768377929161 0.3988707406012982 chr17 81195210 5315531 0.06546606628642256 0.35541242102299575 chr18 78077248 5972845 0.07649917425368272 1.13740086338712 chr19 59128983 4343760 0.07346245072403833 0.631551146635268 chr20 63025520 3849387 0.061076640065801914 0.35254107198943924 chr21 48129895 4884330 0.1014822492340779 0.519571070093439 chr22 51304566 1927398 0.03756776736012151 0.25126802869945425 chrMT 16571 25426 1.534367268119003 1.6422802156102025 chrX 155270560 7871141 0.05069306763626021 0.3254685318863479 chrY 59373566 540224 0.009098729222361344 0.1796105996988605