BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818760.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,238,227 number of mapped reads = 1,204,135 (97.25%) number of supplementary alignments = 9,412 (0.76%) number of secondary alignments = 0 number of mapped bases = 81,758,352 bp number of sequenced bases = 81,723,704 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 523,653 duplication rate = 37.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8776 >>>>>>> ACTG content number of A's = 23,212,800 bp (28.4%) number of C's = 16,705,697 bp (20.44%) number of T's = 24,186,288 bp (29.6%) number of G's = 17,614,336 bp (21.55%) number of N's = 4,583 bp (0.01%) GC percentage = 42% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 422,487 number of insertions = 10,254 mapped reads with insertion percentage = 0.84% number of deletions = 21,148 mapped reads with deletion percentage = 1.74% homopolymer indels = 39.63% >>>>>>> Coverage mean coverageData = 0.0264X std coverageData = 0.3647X There is a 1.32% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% 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 6764454 0.027139166084565142 0.4709195713664814 chr2 243199373 7274922 0.029913407712609523 0.5564892587388955 chr3 198022430 5551950 0.02803697540728088 0.2942474725757551 chr4 191154276 5366052 0.02807183868594182 0.32478039125647973 chr5 180915260 5194161 0.028710463672329243 0.31111376525565565 chr6 171115067 4814973 0.02813880206118845 0.3155699677940815 chr7 159138663 4471309 0.028096937071791284 0.3419284712689863 chr8 146364022 4147369 0.028335986831517924 0.3258628574400422 chr9 141213431 3517765 0.02491098031602957 0.3100296045929988 chr10 135534747 3948220 0.029130684842020624 0.38172053649603727 chr11 135006516 3838715 0.028433553533075397 0.3294181409238638 chr12 133851895 3677328 0.027473111232381133 0.3082933200569425 chr13 115169878 2677584 0.023248995713966113 0.2667169036271888 chr14 107349540 2568212 0.023923828644258745 0.29223604992104 chr15 102531392 2377365 0.023186703639018185 0.27164404413300447 chr16 90354753 2366758 0.026194061977016306 0.4227386551979319 chr17 81195210 2164716 0.026660636754311 0.30105292240111403 chr18 78077248 2199133 0.02816611825252857 0.3789889531419638 chr19 59128983 1583153 0.026774568404127633 0.43192579405374093 chr20 63025520 1792772 0.02844517585892191 0.317494961047446 chr21 48129895 1135979 0.023602357744599275 0.28257552293243143 chr22 51304566 960402 0.01871962039402107 0.2645233449797026 chrMT 16571 11403 0.6881298654275542 1.7528717942590484 chrX 155270560 2536653 0.016336986225849896 0.24054150010649067 chrY 59373566 817004 0.013760399703800847 0.5937048515328902