BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524754.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,893,748 number of mapped reads = 1,708,846 (90.24%) number of supplementary alignments = 5,012 (0.26%) number of secondary alignments = 0 number of mapped bases = 96,818,720 bp number of sequenced bases = 96,788,499 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,639 duplication rate = 3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3012 >>>>>>> ACTG content number of A's = 23,730,590 bp (24.52%) number of C's = 17,713,827 bp (18.3%) number of T's = 31,468,016 bp (32.51%) number of G's = 23,864,649 bp (24.66%) number of N's = 11,417 bp (0.01%) GC percentage = 42.96% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 495,463 number of insertions = 7,097 mapped reads with insertion percentage = 0.41% number of deletions = 18,535 mapped reads with deletion percentage = 1.08% homopolymer indels = 41.25% >>>>>>> Coverage mean coverageData = 0.0313X std coverageData = 0.2686X There is a 2.76% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 7741960 0.031060945681655894 0.3286298459833095 chr2 243199373 8129629 0.033427837003510694 0.47782412346632164 chr3 198022430 6402464 0.032332014105674795 0.20327590308320898 chr4 191154276 6106603 0.031945939833435896 0.23007224212463726 chr5 180915260 5753605 0.03180276224349455 0.19853040163315092 chr6 171115067 5450805 0.03185461745458101 0.22058925968518536 chr7 159138663 5273514 0.033137855380876234 0.30271399570159035 chr8 146364022 4803724 0.032820388059573824 0.23105118027283916 chr9 141213431 4164038 0.029487549240270212 0.23515990189826885 chr10 135534747 4781028 0.03527529364849886 0.3162602279692473 chr11 135006516 4357128 0.03227346448966952 0.23942520565934736 chr12 133851895 4370845 0.03265433784108921 0.203923251172782 chr13 115169878 2976006 0.02584014198573693 0.1789299993378177 chr14 107349540 2911044 0.02711743338630049 0.18923026433170906 chr15 102531392 2826330 0.027565508912626487 0.18769400286284485 chr16 90354753 2974842 0.03292402337705466 0.22301372524351368 chr17 81195210 2804602 0.034541471104022024 0.21748550704132316 chr18 78077248 2525261 0.032343109736654656 0.35417568762232743 chr19 59128983 2184950 0.03695226755379845 0.29242657968352265 chr20 63025520 2101905 0.03335006200662843 0.21314764258784608 chr21 48129895 1262542 0.026231970794866683 0.20353682385510424 chr22 51304566 1226120 0.023898847521680623 0.1729211746042328 chrMT 16571 21214 1.2801882807313982 1.3633027353060523 chrX 155270560 5343008 0.03441095337068405 0.22644288417842384 chrY 59373566 325553 0.005483130320991668 0.1490329373318215