BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004009.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 = 1,923,132 number of mapped reads = 1,688,904 (87.82%) number of supplementary alignments = 12,259 (0.64%) number of secondary alignments = 0 number of mapped bases = 113,404,316 bp number of sequenced bases = 113,359,746 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,559 duplication rate = 3.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.162 >>>>>>> ACTG content number of A's = 31,129,057 bp (27.46%) number of C's = 21,389,632 bp (18.87%) number of T's = 35,464,612 bp (31.29%) number of G's = 25,355,290 bp (22.37%) number of N's = 21,155 bp (0.02%) GC percentage = 41.24% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 985,185 number of insertions = 7,918 mapped reads with insertion percentage = 0.46% number of deletions = 25,783 mapped reads with deletion percentage = 1.51% homopolymer indels = 46.73% >>>>>>> Coverage mean coverageData = 0.0366X std coverageData = 0.2998X There is a 3.1% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 9649558 0.03871427866974101 0.4932477301284935 chr2 243199373 8951613 0.036807714138309064 0.3446088779305951 chr3 198022430 7697061 0.03886964219154365 0.22434612542586016 chr4 191154276 7832037 0.04097233482760281 0.24007049591351523 chr5 180915260 5490421 0.030348025921085927 0.19886406756368247 chr6 171115067 6761545 0.03951460919569403 0.24484168241693005 chr7 159138663 6889522 0.043292571837178245 0.3997360053851944 chr8 146364022 7529340 0.05144256011221118 0.3729790461168196 chr9 141213431 4521935 0.032021989466426884 0.28666541639870535 chr10 135534747 4144808 0.03058114684052201 0.26373223098874177 chr11 135006516 4864871 0.03603434222389681 0.2591881412893403 chr12 133851895 5345778 0.03993800760161072 0.23231975999681115 chr13 115169878 3835131 0.03329977479007141 0.2179131854639729 chr14 107349540 2881004 0.026837599863026893 0.20010520786955693 chr15 102531392 3305372 0.03223765849194752 0.20763014342840166 chr16 90354753 2512334 0.0278052223771781 0.20240943805086342 chr17 81195210 2805537 0.034552986561645696 0.22805214997038686 chr18 78077248 3195507 0.04092750553912966 0.4875340890756588 chr19 59128983 1821929 0.030812791080813955 0.32920930807675347 chr20 63025520 2330036 0.03696972274088338 0.2282286365845402 chr21 48129895 1507307 0.03131747950000722 0.2127560619707383 chr22 51304566 1238737 0.024144771052151577 0.17642091732450554 chrMT 16571 30171 1.8207108804538048 1.8357954303329287 chrX 155270560 7984467 0.05142292911161008 0.2781161490914602 chrY 59373566 278295 0.004687186887174673 0.10903283923056133