BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524280.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 = 1,358,908 number of mapped reads = 1,255,261 (92.37%) number of supplementary alignments = 4,526 (0.33%) number of secondary alignments = 0 number of mapped bases = 73,735,569 bp number of sequenced bases = 73,713,834 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,584 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1784 >>>>>>> ACTG content number of A's = 18,095,550 bp (24.55%) number of C's = 14,236,872 bp (19.31%) number of T's = 23,072,971 bp (31.3%) number of G's = 18,299,319 bp (24.82%) number of N's = 9,122 bp (0.01%) GC percentage = 44.14% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 359,692 number of insertions = 4,332 mapped reads with insertion percentage = 0.34% number of deletions = 13,703 mapped reads with deletion percentage = 1.08% homopolymer indels = 44.1% >>>>>>> Coverage mean coverageData = 0.0238X std coverageData = 0.2563X There is a 2.18% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 6185918 0.024818064545564362 0.5115873818626673 chr2 243199373 6574917 0.0270350902590526 0.2648978987730925 chr3 198022430 5046142 0.02548267890662689 0.169749147580665 chr4 191154276 4969513 0.025997393853747743 0.1872278601136379 chr5 180915260 4751356 0.026262881306972116 0.1724775120926278 chr6 171115067 2896558 0.016927545018580976 0.1573190455195758 chr7 159138663 4291178 0.026965024834976776 0.34838974601363265 chr8 146364022 4040508 0.027605882544003882 0.23762845011730752 chr9 141213431 3266847 0.023134109672613222 0.2208479207403153 chr10 135534747 3140101 0.023168235965349903 0.23266234163434152 chr11 135006516 3303364 0.0244681819653801 0.2260764568181261 chr12 133851895 2567173 0.019179205494251686 0.15314780469131445 chr13 115169878 2473990 0.02148122445697129 0.1561891340946197 chr14 107349540 2353294 0.021921789324854116 0.16676765001797778 chr15 102531392 1942869 0.018949016121813697 0.1460553151192684 chr16 90354753 2235843 0.02474516199496445 0.18210973244964018 chr17 81195210 2038564 0.025106949042929996 0.18106050803812648 chr18 78077248 2104066 0.02694851642311983 0.4380276140522042 chr19 59128983 1497657 0.02532864466821626 0.3507934574099802 chr20 63025520 1621395 0.025726007496645803 0.1738099804488611 chr21 48129895 1047001 0.021753652277861815 0.17003437129792615 chr22 51304566 882941 0.017209793763775332 0.13907510864930198 chrMT 16571 7555 0.4559169633697423 0.7413959363580492 chrX 155270560 4270067 0.027500815350958996 0.19972605681839492 chrY 59373566 226752 0.003819073289281631 0.10942824068502649