BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238272.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 = 3,134,048 number of mapped reads = 2,566,332 (81.89%) number of supplementary alignments = 26,044 (0.83%) number of secondary alignments = 0 number of mapped bases = 165,385,330 bp number of sequenced bases = 165,283,892 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 231,266 duplication rate = 7.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2437 >>>>>>> ACTG content number of A's = 45,439,399 bp (27.49%) number of C's = 31,467,749 bp (19.04%) number of T's = 51,195,889 bp (30.97%) number of G's = 37,140,827 bp (22.47%) number of N's = 40,028 bp (0.02%) GC percentage = 41.51% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 1,650,185 number of insertions = 13,732 mapped reads with insertion percentage = 0.53% number of deletions = 61,566 mapped reads with deletion percentage = 2.36% homopolymer indels = 46.7% >>>>>>> Coverage mean coverageData = 0.0534X std coverageData = 0.4827X There is a 3.6% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 13780672 0.0552884159113088 0.7680471287880328 chr2 243199373 13273048 0.05457681833743872 0.6047690046533064 chr3 198022430 10075328 0.05087973114964805 0.31412134860669144 chr4 191154276 10528833 0.05508029022589063 0.3499853003282092 chr5 180915260 10492008 0.057994046494474816 0.3352537752032042 chr6 171115067 9008980 0.05264866594126396 0.3757511886323553 chr7 159138663 10568288 0.06640930494684374 0.6830262425622508 chr8 146364022 7859787 0.05370026658600568 0.5958260931702998 chr9 141213431 8237846 0.05833613659595878 0.4902822191391608 chr10 135534747 6671183 0.049221200818709614 0.46826948432305127 chr11 135006516 6677754 0.04946245705651718 0.395059161816726 chr12 133851895 9762145 0.07293243775144162 0.3846213683403261 chr13 115169878 5842912 0.050732987665403274 0.3145025117976193 chr14 107349540 5197831 0.048419685822594115 0.34214279105692036 chr15 102531392 4597216 0.044837155824432776 0.3162524045241111 chr16 90354753 4505434 0.04986382952095503 0.34252551154743577 chr17 81195210 4793273 0.059033938085756535 0.37593361373966416 chr18 78077248 4050373 0.051876482634223994 0.8383902356344973 chr19 59128983 3438693 0.058155794764811024 0.5716225621628633 chr20 63025520 3217081 0.05104410086580801 0.32548197851943156 chr21 48129895 2132590 0.044309051578026504 0.3192884833243398 chr22 51304566 1780534 0.03470517614358145 0.25533399789206296 chrMT 16571 11543 0.6965783597851669 1.0229149343367672 chrX 155270560 8394936 0.05406650172447372 0.35186520647394726 chrY 59373566 487042 0.008203010747240615 0.18802081855971828