BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971324.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 88,952,985 number of mapped reads = 67,167,897 (75.51%) number of secondary alignments = 0 number of mapped bases = 2,656,451,364 bp number of sequenced bases = 2,656,208,383 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,917,200 duplication rate = 10.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.0655 >>>>>>> ACTG content number of A's = 768,289,787 bp (28.92%) number of C's = 563,775,012 bp (21.22%) number of T's = 760,529,498 bp (28.63%) number of G's = 563,474,858 bp (21.21%) number of N's = 139,228 bp (0.01%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 8,586,349 number of insertions = 90,002 mapped reads with insertion percentage = 0.13% number of deletions = 191,183 mapped reads with deletion percentage = 0.28% homopolymer indels = 39.29% >>>>>>> Coverage mean coverageData = 0.8581X std coverageData = 7.3508X There is a 35.51% of reference with a coverageData >= 1X There is a 18.96% of reference with a coverageData >= 2X There is a 10.7% of reference with a coverageData >= 3X There is a 6.28% of reference with a coverageData >= 4X There is a 3.83% of reference with a coverageData >= 5X There is a 2.42% of reference with a coverageData >= 6X There is a 1.57% of reference with a coverageData >= 7X There is a 1.06% of reference with a coverageData >= 8X There is a 0.73% of reference with a coverageData >= 9X There is a 0.52% of reference with a coverageData >= 10X There is a 0.38% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 206276363 0.8275861547402122 12.33343725171196 chr2 243199373 225481787 0.9271478960597485 7.512595514127452 chr3 198022430 180758326 0.9128174318434533 2.1558500892241645 chr4 191154276 174184643 0.9112254595863709 2.1697548828734874 chr5 180915260 167884103 0.9279709351217802 2.41555355299346 chr6 171115067 154646875 0.9037595444473631 3.4022512538154226 chr7 159138663 150251157 0.9441524401898488 14.202503184858323 chr8 146364022 138269237 0.9446941612468124 5.626105368550221 chr9 141213431 111097524 0.7867348255280335 8.060479580573643 chr10 135534747 124634555 0.9195764020572526 6.479764930232696 chr11 135006516 123822742 0.9171612279810257 9.24904809203978 chr12 133851895 120174554 0.8978173525298241 2.757287846531648 chr13 115169878 84664177 0.7351243091531277 1.6360585978460327 chr14 107349540 80541928 0.7502773463211859 5.81014354006571 chr15 102531392 73947493 0.7212180733877094 1.8879408350200395 chr16 90354753 72199068 0.7990622031803906 4.14061437820541 chr17 81195210 63832093 0.7861558951568695 3.5866507894740867 chr18 78077248 71564058 0.9165801796702671 17.457729545912155 chr19 59128983 48444075 0.8192949132915072 13.189910050564954 chr20 63025520 51913169 0.8236848978001292 2.4799992950657583 chr21 48129895 32116819 0.6672945993337405 3.3334303030140626 chr22 51304566 25350324 0.4941143835034098 2.1911152793552513 chrMT 16571 71983 4.343914066743105 5.066935708021095 chrX 155270560 164772522 1.0611961597871482 5.245830304880496 chrY 59373566 9551789 0.16087612120181563 1.5324723087229717