BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231758.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 = 4,494,591 number of mapped reads = 4,107,141 (91.38%) number of supplementary alignments = 36,111 (0.8%) number of secondary alignments = 0 number of mapped bases = 282,996,919 bp number of sequenced bases = 282,901,644 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 604,813 duplication rate = 7.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3448 >>>>>>> ACTG content number of A's = 73,060,666 bp (25.83%) number of C's = 52,495,529 bp (18.56%) number of T's = 79,429,340 bp (28.08%) number of G's = 77,855,516 bp (27.52%) number of N's = 60,593 bp (0.02%) GC percentage = 46.08% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,791,613 number of insertions = 18,235 mapped reads with insertion percentage = 0.44% number of deletions = 58,028 mapped reads with deletion percentage = 1.4% homopolymer indels = 47.11% >>>>>>> Coverage mean coverageData = 0.0914X std coverageData = 37.4391X There is a 4.54% of reference with a coverageData >= 1X There is a 1.94% of reference with a coverageData >= 2X There is a 0.9% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 30459581 0.12220463434672847 1.0580554815120597 chr2 243199373 42200051 0.17352039390331817 133.54417618201202 chr3 198022430 13555541 0.06845457355512706 0.43497516642218037 chr4 191154276 12727622 0.06658298347456272 0.45712132691322105 chr5 180915260 15433467 0.08530771257217329 0.48956154968060445 chr6 171115067 11002866 0.0643009770729307 0.5084879757290169 chr7 159138663 18584652 0.11678275819120083 2.022871121390145 chr8 146364022 11311031 0.07728013240849585 0.5779441236875832 chr9 141213431 9519108 0.0674093670311006 0.6057047596562942 chr10 135534747 16334672 0.12052017922754524 0.8139980213134368 chr11 135006516 19648040 0.14553401259536244 1.4052496624166066 chr12 133851895 12468563 0.09315193483065742 0.5247237774141363 chr13 115169878 5337285 0.04634271645230014 0.36851119724179143 chr14 107349540 10349968 0.09641371541974003 0.6263413412826708 chr15 102531392 6861525 0.06692121179823639 0.4476427739604924 chr16 90354753 5873288 0.06500253506309735 0.46899494692862315 chr17 81195210 8769741 0.10800810786744686 0.9488311381923751 chr18 78077248 5879913 0.07530891713806306 1.114548847008709 chr19 59128983 6618239 0.1119288488354349 0.7732763230509853 chr20 63025520 4803063 0.07620822485875563 0.47332754758882134 chr21 48129895 4310596 0.08956171626802843 0.5301256705279611 chr22 51304566 1988494 0.03875861653327308 0.3261520620892371 chrMT 16571 60618 3.6580773640697606 3.557176304326438 chrX 155270560 8329033 0.05364206195945967 0.4988608798647986 chrY 59373566 569962 0.009599591845300313 0.2365268373134477