BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472602.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 8,610,040 number of mapped reads = 7,992,276 (92.83%) number of supplementary alignments = 233,412 (2.71%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,034,606 number of mapped paired reads (second in pair) = 3,957,670 number of mapped paired reads (both in pair) = 7,809,648 number of mapped paired reads (singletons) = 182,628 number of mapped bases = 659,872,206 bp number of sequenced bases = 659,589,974 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,136,339 duplication rate = 12.18% >>>>>>> Insert size mean insert size = 229,186.4056 std insert size = 4,570,488.1502 median insert size = 135 >>>>>>> Mapping quality mean mapping quality = 50.7444 >>>>>>> ACTG content number of A's = 168,584,029 bp (25.56%) number of C's = 132,520,756 bp (20.09%) number of T's = 195,950,770 bp (29.71%) number of G's = 162,105,116 bp (24.58%) number of N's = 429,303 bp (0.07%) GC percentage = 44.67% >>>>>>> Mismatches and indels general error rate = 0.0117 number of mismatches = 7,603,117 number of insertions = 60,035 mapped reads with insertion percentage = 0.74% number of deletions = 149,736 mapped reads with deletion percentage = 1.84% homopolymer indels = 42.99% >>>>>>> Coverage mean coverageData = 0.2132X std coverageData = 1.74X There is a 11.78% of reference with a coverageData >= 1X There is a 5.19% of reference with a coverageData >= 2X There is a 1.89% of reference with a coverageData >= 3X There is a 0.91% of reference with a coverageData >= 4X There is a 0.43% of reference with a coverageData >= 5X There is a 0.24% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% 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 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 0.01% 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 40816782 0.16375799521077222 2.1511188479349093 chr2 243199373 60590081 0.24913748852469286 2.5283310453211527 chr3 198022430 32413157 0.16368427051420387 0.6118142813808467 chr4 191154276 29666426 0.15519624578003163 0.9464267078449436 chr5 180915260 29862335 0.16506255470102413 0.6365820107764931 chr6 171115067 42269823 0.2470257221709179 1.0868313184592742 chr7 159138663 54583158 0.34299118121911076 3.1461909678976676 chr8 146364022 31123875 0.2126470328889978 1.5223014150023457 chr9 141213431 21604007 0.15298833012562382 1.8805527518786667 chr10 135534747 33493726 0.24712279870194467 1.6658249750725456 chr11 135006516 34092829 0.2525272854237643 1.8504786709891037 chr12 133851895 31137805 0.2326287946838556 0.761123202454755 chr13 115169878 35338968 0.30684210675294804 0.904255200849219 chr14 107349540 16068053 0.14967975642932424 3.432733132196137 chr15 102531392 18826858 0.18362042719560465 0.668237397822006 chr16 90354753 22913705 0.2535971184603869 1.0533420933913515 chr17 81195210 19628927 0.24174981504450815 1.2035299085709323 chr18 78077248 14096581 0.18054659149871677 2.94461396453195 chr19 59128983 11731206 0.19840026675243172 1.590864230338242 chr20 63025520 22475866 0.3566153202702651 1.1716073219853793 chr21 48129895 9295902 0.1931419547040358 0.8860325434578602 chr22 51304566 6617555 0.1289856930082987 0.5604279160586991 chrMT 16571 52026 3.1395811960654156 3.16944381787534 chrX 155270560 39774386 0.2561617991201938 1.0803388546974462 chrY 59373566 1398169 0.02354867821144514 0.7204713089158505