BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975218.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 42,424,054 number of mapped reads = 42,299,315 (99.71%) number of supplementary alignments = 103,987 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,173,925 number of mapped paired reads (second in pair) = 21,125,390 number of mapped paired reads (both in pair) = 42,224,242 number of mapped paired reads (singletons) = 75,073 number of mapped bases = 4,147,689,881 bp number of sequenced bases = 4,146,026,015 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,208,319 duplication rate = 32.39% >>>>>>> Insert size mean insert size = 136,584.1039 std insert size = 3,715,464.99 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 55.7921 >>>>>>> ACTG content number of A's = 1,106,544,575 bp (26.69%) number of C's = 939,911,187 bp (22.67%) number of T's = 1,116,232,921 bp (26.92%) number of G's = 983,025,709 bp (23.71%) number of N's = 311,623 bp (0.01%) GC percentage = 46.38% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 29,072,357 number of insertions = 365,566 mapped reads with insertion percentage = 0.85% number of deletions = 1,127,772 mapped reads with deletion percentage = 2.62% homopolymer indels = 49.97% >>>>>>> Coverage mean coverageData = 1.3398X std coverageData = 18.5353X There is a 15.16% of reference with a coverageData >= 1X There is a 6.7% of reference with a coverageData >= 2X There is a 3.73% of reference with a coverageData >= 3X There is a 2.7% of reference with a coverageData >= 4X There is a 2.18% of reference with a coverageData >= 5X There is a 1.91% of reference with a coverageData >= 6X There is a 1.74% of reference with a coverageData >= 7X There is a 1.62% of reference with a coverageData >= 8X There is a 1.52% of reference with a coverageData >= 9X There is a 1.45% of reference with a coverageData >= 10X There is a 1.38% of reference with a coverageData >= 11X There is a 1.32% of reference with a coverageData >= 12X There is a 1.27% of reference with a coverageData >= 13X There is a 1.23% of reference with a coverageData >= 14X There is a 1.18% of reference with a coverageData >= 15X There is a 1.15% of reference with a coverageData >= 16X There is a 1.11% of reference with a coverageData >= 17X There is a 1.08% of reference with a coverageData >= 18X There is a 1.04% of reference with a coverageData >= 19X There is a 1.02% of reference with a coverageData >= 20X There is a 0.99% of reference with a coverageData >= 21X There is a 0.96% of reference with a coverageData >= 22X There is a 0.94% of reference with a coverageData >= 23X There is a 0.91% of reference with a coverageData >= 24X There is a 0.89% of reference with a coverageData >= 25X There is a 0.87% of reference with a coverageData >= 26X There is a 0.85% of reference with a coverageData >= 27X There is a 0.83% of reference with a coverageData >= 28X There is a 0.81% of reference with a coverageData >= 29X There is a 0.79% of reference with a coverageData >= 30X There is a 0.78% of reference with a coverageData >= 31X There is a 0.76% of reference with a coverageData >= 32X There is a 0.75% of reference with a coverageData >= 33X There is a 0.73% of reference with a coverageData >= 34X There is a 0.72% of reference with a coverageData >= 35X There is a 0.7% of reference with a coverageData >= 36X There is a 0.69% of reference with a coverageData >= 37X There is a 0.68% of reference with a coverageData >= 38X There is a 0.66% of reference with a coverageData >= 39X There is a 0.65% of reference with a coverageData >= 40X There is a 0.64% of reference with a coverageData >= 41X There is a 0.63% of reference with a coverageData >= 42X There is a 0.62% of reference with a coverageData >= 43X There is a 0.61% of reference with a coverageData >= 44X There is a 0.6% of reference with a coverageData >= 45X There is a 0.59% of reference with a coverageData >= 46X There is a 0.58% of reference with a coverageData >= 47X There is a 0.57% of reference with a coverageData >= 48X There is a 0.56% of reference with a coverageData >= 49X There is a 0.55% of reference with a coverageData >= 50X There is a 0.54% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 595530690 2.389284679054019 28.475310642606875 chr2 243199373 272209930 1.1192871373068878 14.448898292713867 chr3 198022430 254577272 1.2855981617839958 16.58095035774598 chr4 191154276 140816161 0.7366623648010887 10.52081615385357 chr5 180915260 218727003 1.209002507582832 15.685950793556495 chr6 171115067 256007653 1.4961140330208327 19.3086580084883 chr7 159138663 213931053 1.3443059591370325 20.019270386036958 chr8 146364022 174955618 1.1953457933808351 15.281531870114001 chr9 141213431 180169952 1.275869800231679 17.064439096544724 chr10 135534747 130219051 0.9607798286589933 13.627325226904857 chr11 135006516 180022823 1.3334380319835821 17.010425574192155 chr12 133851895 254707508 1.902905506119282 23.377576780496337 chr13 115169878 46225205 0.401365407368062 6.743176284676025 chr14 107349540 147656504 1.3754740262510674 18.821852635289932 chr15 102531392 89659435 0.87445838051238 12.58561735847722 chr16 90354753 146526064 1.6216752205608929 20.222316662465662 chr17 81195210 204543981 2.5191631501414924 28.189180742306792 chr18 78077248 86086854 1.1025856597814514 14.908915842448327 chr19 59128983 212531870 3.594377227830893 37.79011081814568 chr20 63025520 114966381 1.8241242753728966 22.431480117267498 chr21 48129895 46247574 0.960890814326522 15.453917321882653 chr22 51304566 40088403 0.7813808034162105 11.207530873189059 chrMT 16571 58132 3.508056242833866 5.09101262439498 chrX 155270560 132091649 0.8507192155422123 15.231983454614136 chrY 59373566 9133115 0.15382459931748077 3.4686345862767762