BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013229.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,141,346 number of mapped reads = 1,878,238 (87.71%) number of supplementary alignments = 13,381 (0.62%) number of secondary alignments = 0 number of mapped bases = 125,996,076 bp number of sequenced bases = 125,941,231 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,461 duplication rate = 4.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5993 >>>>>>> ACTG content number of A's = 35,052,030 bp (27.83%) number of C's = 23,180,831 bp (18.41%) number of T's = 40,239,304 bp (31.95%) number of G's = 27,442,054 bp (21.79%) number of N's = 27,012 bp (0.02%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,041,964 number of insertions = 10,426 mapped reads with insertion percentage = 0.55% number of deletions = 30,503 mapped reads with deletion percentage = 1.6% homopolymer indels = 46.09% >>>>>>> Coverage mean coverageData = 0.0407X std coverageData = 0.4197X There is a 3.24% of reference with a coverageData >= 1X There is a 0.57% 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 0.01% 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 4733146 0.018989505346107043 0.5148612451895273 chr2 243199373 18340580 0.07541376350505641 0.6297696877111894 chr3 198022430 15397006 0.0777538483898011 0.3341781385746358 chr4 191154276 5659368 0.02960628513484051 0.3216219855432061 chr5 180915260 4079252 0.022547860252363456 0.18876507738800563 chr6 171115067 9220430 0.05388438412615062 0.3519960062247729 chr7 159138663 3283827 0.02063500432952613 0.5044325130859301 chr8 146364022 4120446 0.028152041353441352 0.37623651459008983 chr9 141213431 11794302 0.08352110643073321 0.5483903118651864 chr10 135534747 4167618 0.030749443166777003 0.5412872987871983 chr11 135006516 4152181 0.030755411835085057 0.28616818095079893 chr12 133851895 3650455 0.027272344556645987 0.22484353848698088 chr13 115169878 3970954 0.034479102252760914 0.22010573015411217 chr14 107349540 2952639 0.02750490593625273 0.2406074368799854 chr15 102531392 3716189 0.03624440210467444 0.2271948896450345 chr16 90354753 3302574 0.03655119282988909 0.2831528363734148 chr17 81195210 5990294 0.07377644567949267 0.3961538880367872 chr18 78077248 3555944 0.04554392081032364 0.9041676039114331 chr19 59128983 2495027 0.0421963455721875 0.452975146432259 chr20 63025520 2400436 0.03808673058151682 0.2496259715568735 chr21 48129895 1455048 0.030231688641747505 0.31078369545701146 chr22 51304566 1569448 0.03059080550452371 0.20666761292975078 chrMT 16571 395068 23.840926920523806 13.786931566525178 chrX 155270560 5278879 0.033997938823689434 0.2536030315350735 chrY 59373566 314965 0.005304801803550085 0.2663840703778679