BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927031.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 = 31,892,094 number of mapped reads = 31,195,088 (97.81%) number of supplementary alignments = 493,357 (1.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,673,242 number of mapped paired reads (second in pair) = 15,521,846 number of mapped paired reads (both in pair) = 30,774,930 number of mapped paired reads (singletons) = 420,158 number of mapped bases = 2,877,119,432 bp number of sequenced bases = 2,874,971,073 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,943,912 duplication rate = 7.08% >>>>>>> Insert size mean insert size = 157,951.5531 std insert size = 3,878,632.22 median insert size = 190 >>>>>>> Mapping quality mean mapping quality = 53.3176 >>>>>>> ACTG content number of A's = 816,480,483 bp (28.4%) number of C's = 568,068,948 bp (19.76%) number of T's = 833,940,889 bp (29.01%) number of G's = 656,087,624 bp (22.82%) number of N's = 393,129 bp (0.01%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 30,610,118 number of insertions = 468,223 mapped reads with insertion percentage = 1.48% number of deletions = 1,512,951 mapped reads with deletion percentage = 4.72% homopolymer indels = 52.56% >>>>>>> Coverage mean coverageData = 0.9294X std coverageData = 4.0972X There is a 34.05% of reference with a coverageData >= 1X There is a 19.87% of reference with a coverageData >= 2X There is a 12.1% of reference with a coverageData >= 3X There is a 7.78% of reference with a coverageData >= 4X There is a 5.16% of reference with a coverageData >= 5X There is a 3.5% of reference with a coverageData >= 6X There is a 2.42% of reference with a coverageData >= 7X There is a 1.7% of reference with a coverageData >= 8X There is a 1.21% of reference with a coverageData >= 9X There is a 0.87% of reference with a coverageData >= 10X There is a 0.63% of reference with a coverageData >= 11X There is a 0.47% of reference with a coverageData >= 12X There is a 0.35% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% 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 0.01% 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 0.01% 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 232400437 0.932396621792168 4.633810020678364 chr2 243199373 248822434 1.0231211985896034 5.615167433907653 chr3 198022430 194274646 0.981073941977179 1.995593863567134 chr4 191154276 174335664 0.9120155073067787 2.7815254301283887 chr5 180915260 174840015 0.9664193888343084 1.9465180371193054 chr6 171115067 163526189 0.9556504395957137 1.9880628494681034 chr7 159138663 148296569 0.931870145220461 2.479899969136133 chr8 146364022 144506733 0.9873104812602103 2.313840874868273 chr9 141213431 120944643 0.856466995692499 4.193087010906725 chr10 135534747 141732638 1.045729166410736 7.170996163715034 chr11 135006516 136888949 1.0139432751527342 2.841836235399816 chr12 133851895 128964895 0.9634894971042435 1.9752569245490827 chr13 115169878 87882685 0.7630700537861124 1.7441979690255005 chr14 107349540 87525523 0.8153320731509422 1.9031703649518068 chr15 102531392 85819811 0.837010103208196 1.9130215264128032 chr16 90354753 89408184 0.9895238604658684 4.982021214380161 chr17 81195210 72696089 0.8953248473647645 2.7678379705049387 chr18 78077248 78391847 1.004029330029665 4.410801373519405 chr19 59128983 46269374 0.7825159786698851 2.710318788015398 chr20 63025520 68230488 1.0825850861682695 2.263149692037056 chr21 48129895 36206130 0.752258653379568 2.4564455434982575 chr22 51304566 35087269 0.6839014874426577 1.8132202837529388 chrMT 16571 12326999 743.8898678414097 571.1601809675611 chrX 155270560 163194691 1.0510343428915307 2.3961120039356922 chrY 59373566 4546530 0.07657498624893105 2.1448006769835923