BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063583.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 = 3,237,726 number of mapped reads = 2,848,969 (87.99%) number of supplementary alignments = 24,068 (0.74%) number of secondary alignments = 0 number of mapped bases = 184,120,948 bp number of sequenced bases = 184,049,039 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 191,289 duplication rate = 5.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4007 >>>>>>> ACTG content number of A's = 47,819,430 bp (25.98%) number of C's = 34,254,199 bp (18.61%) number of T's = 57,961,065 bp (31.49%) number of G's = 44,009,785 bp (23.91%) number of N's = 4,560 bp (0%) GC percentage = 42.52% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,503,085 number of insertions = 13,149 mapped reads with insertion percentage = 0.46% number of deletions = 45,441 mapped reads with deletion percentage = 1.58% homopolymer indels = 45.91% >>>>>>> Coverage mean coverageData = 0.0595X std coverageData = 0.5632X There is a 4.74% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 23118396 0.09275160843029555 1.0943936380458834 chr2 243199373 18969546 0.07799997905422232 0.860852301333571 chr3 198022430 11002664 0.05556271579941727 0.2833451022038148 chr4 191154276 11004350 0.05756789871653198 0.33907656352614923 chr5 180915260 6942061 0.0383718930067038 0.2365421991421131 chr6 171115067 11811080 0.06902419644904793 0.4157145885004901 chr7 159138663 12919786 0.08118571412152684 0.8072902883762376 chr8 146364022 5355852 0.03659268122599145 0.5819153239583839 chr9 141213431 5696084 0.04033670140059128 0.4751293377403888 chr10 135534747 9899270 0.07303861348558831 0.3914491634897456 chr11 135006516 11325479 0.08388838802417507 0.5241568031299053 chr12 133851895 5160575 0.038554366376359485 0.2654289030014285 chr13 115169878 4210116 0.03655570426149101 0.23995414183685143 chr14 107349540 4340531 0.04043362458749241 0.2862353172511587 chr15 102531392 3003302 0.029291536391118148 0.24594299723589508 chr16 90354753 3946879 0.0436820296548207 0.2768024815884105 chr17 81195210 6261320 0.07711440120667216 0.37799090383829415 chr18 78077248 3939183 0.05045238018635083 0.7994686980792086 chr19 59128983 4585990 0.07755908807022777 0.7497987060398769 chr20 63025520 2657550 0.042166252654480284 0.2782810477134203 chr21 48129895 3167838 0.06581851051202169 0.32485612216256776 chr22 51304566 2510045 0.04892439787912834 0.2635184076766361 chrMT 16571 200690 12.1109166616378 9.51787125796425 chrX 155270560 11590419 0.07464659752627929 0.4351190488452264 chrY 59373566 501942 0.008453964176583229 0.17763855247401872