BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695917.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 435,889,172 number of mapped reads = 432,435,277 (99.21%) number of supplementary alignments = 5,502,855 (1.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 217,141,769 number of mapped paired reads (second in pair) = 215,293,508 number of mapped paired reads (both in pair) = 429,903,508 number of mapped paired reads (singletons) = 2,531,769 number of mapped bases = 42,879,216,108 bp number of sequenced bases = 42,869,620,277 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,318,555 duplication rate = 13.47% >>>>>>> Insert size mean insert size = 80,971.5279 std insert size = 2,717,043.0179 median insert size = 325 >>>>>>> Mapping quality mean mapping quality = 53.8532 >>>>>>> ACTG content number of A's = 12,734,700,670 bp (29.71%) number of C's = 8,609,659,963 bp (20.08%) number of T's = 12,614,523,494 bp (29.43%) number of G's = 8,900,594,472 bp (20.76%) number of N's = 10,141,678 bp (0.02%) GC percentage = 40.85% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 244,520,594 number of insertions = 4,273,074 mapped reads with insertion percentage = 0.97% number of deletions = 4,165,991 mapped reads with deletion percentage = 0.94% homopolymer indels = 45.51% >>>>>>> Coverage mean coverageData = 13.8512X std coverageData = 17.0476X There is a 90.85% of reference with a coverageData >= 1X There is a 88.87% of reference with a coverageData >= 2X There is a 86.21% of reference with a coverageData >= 3X There is a 82.94% of reference with a coverageData >= 4X There is a 79.16% of reference with a coverageData >= 5X There is a 75% of reference with a coverageData >= 6X There is a 70.6% of reference with a coverageData >= 7X There is a 66.07% of reference with a coverageData >= 8X There is a 61.52% of reference with a coverageData >= 9X There is a 57.03% of reference with a coverageData >= 10X There is a 52.67% of reference with a coverageData >= 11X There is a 48.49% of reference with a coverageData >= 12X There is a 44.53% of reference with a coverageData >= 13X There is a 40.8% of reference with a coverageData >= 14X There is a 37.31% of reference with a coverageData >= 15X There is a 34.08% of reference with a coverageData >= 16X There is a 31.09% of reference with a coverageData >= 17X There is a 28.33% of reference with a coverageData >= 18X There is a 25.81% of reference with a coverageData >= 19X There is a 23.5% of reference with a coverageData >= 20X There is a 21.39% of reference with a coverageData >= 21X There is a 19.47% of reference with a coverageData >= 22X There is a 17.72% of reference with a coverageData >= 23X There is a 16.12% of reference with a coverageData >= 24X There is a 14.68% of reference with a coverageData >= 25X There is a 13.37% of reference with a coverageData >= 26X There is a 12.17% of reference with a coverageData >= 27X There is a 11.09% of reference with a coverageData >= 28X There is a 10.11% of reference with a coverageData >= 29X There is a 9.22% of reference with a coverageData >= 30X There is a 8.41% of reference with a coverageData >= 31X There is a 7.68% of reference with a coverageData >= 32X There is a 7.02% of reference with a coverageData >= 33X There is a 6.41% of reference with a coverageData >= 34X There is a 5.86% of reference with a coverageData >= 35X There is a 5.37% of reference with a coverageData >= 36X There is a 4.91% of reference with a coverageData >= 37X There is a 4.5% of reference with a coverageData >= 38X There is a 4.13% of reference with a coverageData >= 39X There is a 3.79% of reference with a coverageData >= 40X There is a 3.47% of reference with a coverageData >= 41X There is a 3.19% of reference with a coverageData >= 42X There is a 2.93% of reference with a coverageData >= 43X There is a 2.7% of reference with a coverageData >= 44X There is a 2.48% of reference with a coverageData >= 45X There is a 2.29% of reference with a coverageData >= 46X There is a 2.11% of reference with a coverageData >= 47X There is a 1.94% of reference with a coverageData >= 48X There is a 1.79% of reference with a coverageData >= 49X There is a 1.66% of reference with a coverageData >= 50X There is a 1.53% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3540480174 14.204498908750963 17.834297572842864 chr2 243199373 3805971078 15.649592476539814 19.79211587428963 chr3 198022430 3087380225 15.591063219454483 12.343693021602677 chr4 191154276 3121195574 16.328149384427057 16.801374064500273 chr5 180915260 2680884945 14.818456690718074 11.668111386330105 chr6 171115067 2822722471 16.496048655960845 15.069053909332606 chr7 159138663 2156074336 13.548400466327909 12.080699440980725 chr8 146364022 1963328861 13.414012775625967 11.504422059234859 chr9 141213431 1812648597 12.8362336653374 15.354403673981787 chr10 135534747 2042815366 15.072263100177551 19.181816878434873 chr11 135006516 2178010101 16.132629487305636 14.419559675669294 chr12 133851895 2098569812 15.678297359929047 12.843462901184756 chr13 115169878 1493048677 12.9638817278247 12.432136572404044 chr14 107349540 1292806661 12.04296414311603 12.470751762914668 chr15 102531392 1342587432 13.094403633962171 13.4318845390978 chr16 90354753 1061292303 11.745838129843596 19.974401220274704 chr17 81195210 981658955 12.090109194865066 15.146434072482744 chr18 78077248 1192203974 15.269544003395202 18.614692410513264 chr19 59128983 589006274 9.961380090031314 13.01400057453566 chr20 63025520 758379770 12.032899847553816 13.117647251749789 chr21 48129895 579157450 12.033216569452312 24.076740044955315 chr22 51304566 428562917 8.353309469570409 11.748497353567721 chrMT 16571 49883426 3010.284593567075 788.095072647812 chrX 155270560 1529455352 9.850259778801597 9.168548815136042 chrY 59373566 271091377 4.565859780091363 19.127034332880477