BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472604.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 = 16,833,956 number of mapped reads = 16,729,331 (99.38%) number of supplementary alignments = 82,272 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,383,157 number of mapped paired reads (second in pair) = 8,346,174 number of mapped paired reads (both in pair) = 16,655,810 number of mapped paired reads (singletons) = 73,521 number of mapped bases = 1,645,837,515 bp number of sequenced bases = 1,645,642,845 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,911,981 duplication rate = 50.28% >>>>>>> Insert size mean insert size = 17,531.448 std insert size = 1,304,320.9325 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 54.9256 >>>>>>> ACTG content number of A's = 449,170,363 bp (27.29%) number of C's = 375,081,497 bp (22.79%) number of T's = 450,651,467 bp (27.38%) number of G's = 370,421,527 bp (22.51%) number of N's = 317,991 bp (0.02%) GC percentage = 45.3% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 9,275,657 number of insertions = 102,779 mapped reads with insertion percentage = 0.6% number of deletions = 79,246 mapped reads with deletion percentage = 0.47% homopolymer indels = 45.49% >>>>>>> Coverage mean coverageData = 0.5317X std coverageData = 29.603X There is a 3.19% of reference with a coverageData >= 1X There is a 1.53% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.27% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 163118226 0.6544345821308907 20.620136408329785 chr2 243199373 88926378 0.3656521680259431 13.859251855479624 chr3 198022430 180323008 0.9106191051185464 41.74910824923469 chr4 191154276 111566969 0.5836488271912892 39.9285733637333 chr5 180915260 90944826 0.502692951385085 23.04668137757745 chr6 171115067 112544897 0.657714711937085 29.677905925675432 chr7 159138663 96974645 0.6093719978029475 24.1449511131969 chr8 146364022 82672632 0.5648425813278074 25.17309744185885 chr9 141213431 92439354 0.6546073793788071 31.461994926417916 chr10 135534747 38393357 0.28327316684333353 12.487295971549004 chr11 135006516 75761679 0.5611705363909991 74.29895140821078 chr12 133851895 65656797 0.49051824779918135 27.032454302397763 chr13 115169878 50202933 0.4359033270834931 25.30277315016081 chr14 107349540 38618803 0.3597481926797264 17.68636108313384 chr15 102531392 30884948 0.3012243118673352 13.376451899765726 chr16 90354753 83648098 0.9257741869982202 35.91123227078017 chr17 81195210 72696332 0.895327840152147 30.80615071754184 chr18 78077248 31745807 0.4065948507816259 31.470269371217746 chr19 59128983 31898421 0.5394718356647534 14.755085206112652 chr20 63025520 28227601 0.44787573351239307 15.650712145981448 chr21 48129895 10634778 0.22095992521903488 15.254941786288445 chr22 51304566 21460921 0.41830430843133926 17.319416552709523 chrMT 16571 468 0.028242109709733874 0.16566379492477296 chrX 155270560 42850875 0.27597552942425146 11.649329200462722 chrY 59373566 3644762 0.06138694785487535 4.648829454501899