BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006145.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 9,167,146 number of mapped reads = 7,908,475 (86.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,016,547 number of mapped paired reads (second in pair) = 3,891,928 number of mapped paired reads (both in pair) = 7,247,342 number of mapped paired reads (singletons) = 661,133 number of mapped bases = 305,930,908 bp number of sequenced bases = 305,898,639 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 279,332 duplication rate = 2.82% >>>>>>> Insert size mean insert size = 61,825.2891 std insert size = 2,392,912.4983 median insert size = 124 >>>>>>> Mapping quality mean mapping quality = 47.7206 >>>>>>> ACTG content number of A's = 85,166,354 bp (27.84%) number of C's = 65,974,822 bp (21.57%) number of T's = 86,504,184 bp (28.28%) number of G's = 68,239,513 bp (22.31%) number of N's = 13,766 bp (0%) GC percentage = 43.88% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 1,313,845 number of insertions = 8,588 mapped reads with insertion percentage = 0.11% number of deletions = 24,864 mapped reads with deletion percentage = 0.31% homopolymer indels = 45.92% >>>>>>> Coverage mean coverageData = 0.0988X std coverageData = 0.5585X There is a 7.68% of reference with a coverageData >= 1X There is a 1.59% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% 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 25818769 0.10358557541968973 0.9580370751619464 chr2 243199373 27001425 0.11102588245570846 0.5342634725229373 chr3 198022430 21474762 0.10844610885746629 0.40066388864502994 chr4 191154276 19969384 0.10446736749953739 0.43357493276995457 chr5 180915260 19188275 0.10606222493337489 0.39801878584418393 chr6 171115067 17895381 0.10458097766457936 0.42955725507217773 chr7 159138663 17289452 0.1086439440552545 0.7539592204200324 chr8 146364022 15743489 0.10756392715144163 0.9034227038546799 chr9 141213431 13027537 0.09225423465562564 0.4578031195449379 chr10 135534747 14729940 0.10868017483369044 0.508620146048703 chr11 135006516 14212896 0.10527562980737908 0.5585228297980541 chr12 133851895 14107129 0.10539356951203417 0.4002618636682262 chr13 115169878 9931500 0.08623348546049515 0.35548343842539737 chr14 107349540 9459071 0.08811468591295314 0.3825551904961703 chr15 102531392 9032476 0.08809473687824311 0.3631139907635385 chr16 90354753 8977261 0.09935571402646633 0.4231635526790918 chr17 81195210 8408492 0.10355896610157175 0.45577825265688965 chr18 78077248 8112692 0.10390596758738217 0.6907595580676483 chr19 59128983 5879745 0.09943930542488782 0.7347229191349844 chr20 63025520 6623850 0.10509790319857734 0.4086418855912631 chr21 48129895 4053311 0.08421607817760667 0.40466741759475816 chr22 51304566 3609302 0.0703505025264223 0.3701721127312974 chrMT 16571 146854 8.862108502806107 5.522945977103395 chrX 155270560 8696104 0.05600613535495718 0.3337799316128318 chrY 59373566 2541811 0.042810482361797166 0.4105421132283364