BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472413.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 = 18,074,944 number of mapped reads = 17,909,856 (99.09%) number of supplementary alignments = 73,506 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,979,863 number of mapped paired reads (second in pair) = 8,929,993 number of mapped paired reads (both in pair) = 17,810,048 number of mapped paired reads (singletons) = 99,808 number of mapped bases = 1,758,249,617 bp number of sequenced bases = 1,758,013,502 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,256,860 duplication rate = 46.81% >>>>>>> Insert size mean insert size = 19,601.129 std insert size = 1,389,089.4365 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 55.0495 >>>>>>> ACTG content number of A's = 482,073,088 bp (27.42%) number of C's = 398,173,328 bp (22.65%) number of T's = 482,933,154 bp (27.47%) number of G's = 394,624,168 bp (22.45%) number of N's = 209,764 bp (0.01%) GC percentage = 45.1% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 9,602,571 number of insertions = 103,542 mapped reads with insertion percentage = 0.57% number of deletions = 92,856 mapped reads with deletion percentage = 0.51% homopolymer indels = 45.37% >>>>>>> Coverage mean coverageData = 0.568X std coverageData = 18.1526X There is a 5.05% of reference with a coverageData >= 1X There is a 2.17% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.4% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 217773292 0.873712134101363 23.177727738506622 chr2 243199373 109892250 0.45186074554558986 14.467661682434384 chr3 198022430 188056647 0.9496734637586257 22.323379568855973 chr4 191154276 52760922 0.2760122509631958 8.116859353173675 chr5 180915260 85982956 0.47526646453151605 20.362399357604755 chr6 171115067 112682565 0.6585192465839376 18.519533697640757 chr7 159138663 74013488 0.46508803457774434 14.324852331707564 chr8 146364022 87800121 0.5998750225653132 15.63010993033479 chr9 141213431 70627971 0.5001505203849909 12.234091021011716 chr10 135534747 47429261 0.34994170904380706 10.714254434140242 chr11 135006516 81213298 0.6015509503259828 16.848857560852665 chr12 133851895 136975230 1.0233342606019884 28.229252569955886 chr13 115169878 37545746 0.3260031759345964 12.74625630194283 chr14 107349540 41452258 0.38614285631778206 19.77808397057766 chr15 102531392 46754276 0.45599962204746036 12.124121925576592 chr16 90354753 117023217 1.2951528626280457 43.30058401926059 chr17 81195210 50228057 0.6186086223559247 14.970229833566611 chr18 78077248 25928898 0.33209287806865323 11.1378090737664 chr19 59128983 45635301 0.7717924220005611 17.41397984512979 chr20 63025520 39892322 0.6329550632823021 17.13482040049343 chr21 48129895 12472451 0.25914145459905946 14.471689137214161 chr22 51304566 22026283 0.4293240293661192 10.661851700399197 chrMT 16571 7475 0.45108925230824937 0.783293200035211 chrX 155270560 53137817 0.34222725157943656 9.680611492856492 chrY 59373566 937515 0.015790107671821495 0.7169005980304123