BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038457.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 13,144,228 number of mapped reads = 12,097,465 (92.04%) number of supplementary alignments = 204,982 (1.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,115,255 number of mapped paired reads (second in pair) = 5,982,210 number of mapped paired reads (both in pair) = 11,942,772 number of mapped paired reads (singletons) = 154,693 number of mapped bases = 1,719,416,579 bp number of sequenced bases = 1,718,237,464 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,812,206 duplication rate = 9.08% >>>>>>> Insert size mean insert size = 74,145.4547 std insert size = 2,535,562.7061 median insert size = 258 >>>>>>> Mapping quality mean mapping quality = 53.5563 >>>>>>> ACTG content number of A's = 492,907,695 bp (28.69%) number of C's = 357,942,572 bp (20.83%) number of T's = 492,903,395 bp (28.69%) number of G's = 374,448,270 bp (21.79%) number of N's = 35,532 bp (0%) GC percentage = 42.62% >>>>>>> Mismatches and indels general error rate = 0.0142 number of mismatches = 23,524,572 number of insertions = 288,108 mapped reads with insertion percentage = 2.25% number of deletions = 578,186 mapped reads with deletion percentage = 4.6% homopolymer indels = 46.77% >>>>>>> Coverage mean coverageData = 0.5554X std coverageData = 9.1962X There is a 25.07% of reference with a coverageData >= 1X There is a 12.46% of reference with a coverageData >= 2X There is a 6.01% of reference with a coverageData >= 3X There is a 3.28% of reference with a coverageData >= 4X There is a 1.76% of reference with a coverageData >= 5X There is a 1% of reference with a coverageData >= 6X There is a 0.58% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.22% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 104409353 0.4188930506215268 13.054165171300856 chr2 243199373 171287448 0.7043087565854868 10.040220110929022 chr3 198022430 111844404 0.5648067443672922 1.2764673070788732 chr4 191154276 94260048 0.49310980623839146 7.003399524705539 chr5 180915260 93412209 0.5163312868135059 1.2843749270875726 chr6 171115067 124864944 0.7297133220886972 16.04047572171069 chr7 159138663 115737419 0.7272740440203397 8.651332370353296 chr8 146364022 83253626 0.5688120950926041 2.3743062515405584 chr9 141213431 70397905 0.49852131274963496 14.010403062262741 chr10 135534747 71544680 0.5278696539714646 17.708103509397834 chr11 135006516 100112441 0.7415378454770287 9.593802293391903 chr12 133851895 65838922 0.4918788934590728 1.1716458202069215 chr13 115169878 82185413 0.7136016328852931 1.4850178586842104 chr14 107349540 32770460 0.30526875103516976 1.0040359633714175 chr15 102531392 35239324 0.3436930223282251 0.9354749413107638 chr16 90354753 69008698 0.7637528265945235 12.650873589422831 chr17 81195210 41425595 0.5101975227356392 8.31387643531953 chr18 78077248 27811096 0.3561997472042047 11.242516155202619 chr19 59128983 24135465 0.4081833269481398 7.432365880667242 chr20 63025520 57071195 0.9055251745642082 2.6688031159208556 chr21 48129895 15477948 0.321586988710447 3.0250357449293177 chr22 51304566 11468235 0.22353244348660897 0.785635234708626 chrMT 16571 5604380 338.2040914851246 245.55198961504746 chrX 155270560 85866717 0.5530135075187467 2.4331658035410526 chrY 59373566 24388654 0.41076619854700996 10.678738497205167