BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927035.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 17,242,400 number of mapped reads = 16,643,361 (96.53%) number of supplementary alignments = 684,057 (3.97%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,361,795 number of mapped paired reads (second in pair) = 8,281,566 number of mapped paired reads (both in pair) = 16,306,574 number of mapped paired reads (singletons) = 336,787 number of mapped bases = 1,476,973,552 bp number of sequenced bases = 1,475,846,705 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,441,692 duplication rate = 7.12% >>>>>>> Insert size mean insert size = 409,787.7253 std insert size = 6,250,468.7829 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 52.3313 >>>>>>> ACTG content number of A's = 423,103,471 bp (28.67%) number of C's = 280,461,123 bp (19%) number of T's = 436,136,470 bp (29.55%) number of G's = 335,997,493 bp (22.77%) number of N's = 148,148 bp (0.01%) GC percentage = 41.77% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 16,086,556 number of insertions = 256,800 mapped reads with insertion percentage = 1.52% number of deletions = 769,691 mapped reads with deletion percentage = 4.51% homopolymer indels = 51.62% >>>>>>> Coverage mean coverageData = 0.4771X std coverageData = 1.7218X There is a 24.57% of reference with a coverageData >= 1X There is a 11.05% of reference with a coverageData >= 2X There is a 5.11% of reference with a coverageData >= 3X There is a 2.65% of reference with a coverageData >= 4X There is a 1.44% of reference with a coverageData >= 5X There is a 0.83% of reference with a coverageData >= 6X There is a 0.5% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.09% 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 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 121101737 0.48586333110881197 1.9576283664375629 chr2 243199373 131441937 0.5404698843528679 3.045917627947191 chr3 198022430 96735546 0.4885080240657586 1.1301331827888472 chr4 191154276 96009359 0.5022611108108301 1.6119898012940104 chr5 180915260 88556945 0.48949405926288364 1.1262266013967939 chr6 171115067 90156085 0.5268740303272067 1.2128434371093373 chr7 159138663 80358859 0.5049612550785348 1.4420040913673116 chr8 146364022 78254980 0.5346599453245415 1.3474433912397699 chr9 141213431 62539992 0.4428756638594809 1.8163702514225422 chr10 135534747 69135369 0.5100933194644175 2.719602171294558 chr11 135006516 72198005 0.5347742252677641 1.5290376184408563 chr12 133851895 66742689 0.4986308860251848 1.166398520443832 chr13 115169878 48388526 0.42014914698442246 1.0573029375115144 chr14 107349540 42561369 0.3964746285824792 1.0572431571219951 chr15 102531392 41535340 0.40509876233807496 1.060961973368656 chr16 90354753 43823376 0.48501461788069966 2.7400522838976267 chr17 81195210 36645732 0.45132874217580077 1.2759513044124657 chr18 78077248 37133428 0.4755985764252347 1.7882249292072063 chr19 59128983 20703813 0.35014661084226667 1.4025277422522218 chr20 63025520 32367021 0.5135542078827751 1.2418647813723538 chr21 48129895 17041855 0.3540804524921569 1.3306876266655139 chr22 51304566 15605006 0.3041640777158119 0.9703385506951054 chrMT 16571 344793 20.80701225031682 18.162663186087585 chrX 155270560 85050588 0.5477573340367936 1.284160575068034 chrY 59373566 2541202 0.04280022527196699 1.3804794717057212