BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173951.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 1,264,570 number of mapped reads = 1,235,376 (97.69%) number of supplementary alignments = 123,233 (9.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 618,867 number of mapped paired reads (second in pair) = 616,509 number of mapped paired reads (both in pair) = 1,216,158 number of mapped paired reads (singletons) = 19,218 number of mapped bases = 146,542,277 bp number of sequenced bases = 146,441,844 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 921,681 duplication rate = 62.41% >>>>>>> Insert size mean insert size = 1,055,370.3271 std insert size = 9,705,979.8069 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 52.8412 >>>>>>> ACTG content number of A's = 44,346,048 bp (30.28%) number of C's = 28,349,851 bp (19.36%) number of T's = 44,239,802 bp (30.21%) number of G's = 29,504,171 bp (20.15%) number of N's = 1,972 bp (0%) GC percentage = 39.51% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 1,585,116 number of insertions = 18,580 mapped reads with insertion percentage = 1.44% number of deletions = 41,347 mapped reads with deletion percentage = 3.25% homopolymer indels = 41.76% >>>>>>> Coverage mean coverageData = 0.0473X std coverageData = 0.8629X There is a 1.12% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.29% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 11216055 0.04499910553883835 0.665880785159143 chr2 243199373 13108783 0.05390138485266572 2.0702640979164846 chr3 198022430 10539210 0.05322230416019034 0.6407776787138496 chr4 191154276 9643258 0.050447513923256415 0.7614460274395933 chr5 180915260 9291959 0.05136083600686863 0.6265289041241878 chr6 171115067 8901368 0.05201977918168948 0.678029484050923 chr7 159138663 8017001 0.050377456042847366 0.7177061521840904 chr8 146364022 7540311 0.05151751705757307 0.7277830490909638 chr9 141213431 6583270 0.046619290767037594 0.7661105857553967 chr10 135534747 7622637 0.056241201379894114 0.823734464075693 chr11 135006516 6843778 0.0506922051080853 0.6157022105819213 chr12 133851895 6085118 0.045461575273177866 0.5897016968404837 chr13 115169878 5155700 0.0447660455106152 0.5884657947084968 chr14 107349540 4450559 0.04145857541634552 0.5596075751980023 chr15 102531392 4306323 0.04200004424010941 0.5519298579908677 chr16 90354753 4021957 0.04451295439875753 0.6166463504195268 chr17 81195210 4026089 0.0495853018915771 0.6283888294181186 chr18 78077248 4235567 0.05424841562038662 0.9308152697494063 chr19 59128983 2748523 0.046483515537549494 0.6180377502270364 chr20 63025520 2948748 0.04678657153483224 0.6081640546853894 chr21 48129895 2117312 0.04399161893039659 0.6398647933457908 chr22 51304566 1738582 0.033887471146330325 0.4991098563857493 chrMT 16571 303494 18.31476676120934 17.997843573783232 chrX 155270560 3943867 0.025399966355502294 0.44096886798049256 chrY 59373566 1152808 0.019416182615677825 0.574825698500017