BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777294.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 86,550,558 number of mapped reads = 85,289,432 (98.54%) number of supplementary alignments = 3,169,814 (3.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 42,736,292 number of mapped paired reads (second in pair) = 42,553,140 number of mapped paired reads (both in pair) = 84,922,740 number of mapped paired reads (singletons) = 366,692 number of mapped bases = 8,237,496,072 bp number of sequenced bases = 8,234,706,847 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,764,311 duplication rate = 13.1% >>>>>>> Insert size mean insert size = 122,790.6213 std insert size = 3,367,526.0183 median insert size = 153 >>>>>>> Mapping quality mean mapping quality = 53.1178 >>>>>>> ACTG content number of A's = 2,389,436,476 bp (29.02%) number of C's = 1,727,554,102 bp (20.98%) number of T's = 2,333,957,304 bp (28.34%) number of G's = 1,783,622,237 bp (21.66%) number of N's = 136,728 bp (0%) GC percentage = 42.64% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 50,306,556 number of insertions = 1,785,450 mapped reads with insertion percentage = 2.04% number of deletions = 1,087,499 mapped reads with deletion percentage = 1.23% homopolymer indels = 44.98% >>>>>>> Coverage mean coverageData = 2.661X std coverageData = 28.2904X There is a 44.5% of reference with a coverageData >= 1X There is a 34.77% of reference with a coverageData >= 2X There is a 26.87% of reference with a coverageData >= 3X There is a 21.64% of reference with a coverageData >= 4X There is a 17.61% of reference with a coverageData >= 5X There is a 14.53% of reference with a coverageData >= 6X There is a 12.11% of reference with a coverageData >= 7X There is a 10.18% of reference with a coverageData >= 8X There is a 8.63% of reference with a coverageData >= 9X There is a 7.37% of reference with a coverageData >= 10X There is a 6.34% of reference with a coverageData >= 11X There is a 5.48% of reference with a coverageData >= 12X There is a 4.76% of reference with a coverageData >= 13X There is a 4.15% of reference with a coverageData >= 14X There is a 3.64% of reference with a coverageData >= 15X There is a 3.2% of reference with a coverageData >= 16X There is a 2.83% of reference with a coverageData >= 17X There is a 2.5% of reference with a coverageData >= 18X There is a 2.22% of reference with a coverageData >= 19X There is a 1.98% of reference with a coverageData >= 20X There is a 1.77% of reference with a coverageData >= 21X There is a 1.58% of reference with a coverageData >= 22X There is a 1.42% of reference with a coverageData >= 23X There is a 1.28% of reference with a coverageData >= 24X There is a 1.15% of reference with a coverageData >= 25X There is a 1.04% of reference with a coverageData >= 26X There is a 0.94% of reference with a coverageData >= 27X There is a 0.85% of reference with a coverageData >= 28X There is a 0.77% of reference with a coverageData >= 29X There is a 0.7% of reference with a coverageData >= 30X There is a 0.63% of reference with a coverageData >= 31X There is a 0.58% of reference with a coverageData >= 32X There is a 0.53% of reference with a coverageData >= 33X There is a 0.48% of reference with a coverageData >= 34X There is a 0.44% of reference with a coverageData >= 35X There is a 0.4% of reference with a coverageData >= 36X There is a 0.37% of reference with a coverageData >= 37X There is a 0.34% of reference with a coverageData >= 38X There is a 0.31% of reference with a coverageData >= 39X There is a 0.29% of reference with a coverageData >= 40X There is a 0.27% of reference with a coverageData >= 41X There is a 0.25% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 695090564 2.788721493295698 59.17757257863127 chr2 243199373 712323121 2.9289677527252507 19.778439514302182 chr3 198022430 556249378 2.809022078963479 9.583713784569301 chr4 191154276 537741257 2.8131270105618773 23.421938111493294 chr5 180915260 498176861 2.753647541948645 6.072122342563553 chr6 171115067 470940568 2.7521864453934963 14.557002891093493 chr7 159138663 435595862 2.737209511430921 20.98807398989442 chr8 146364022 413095152 2.8223818009045964 10.818053249448713 chr9 141213431 349149513 2.4724950773273116 25.382216537698785 chr10 135534747 450907840 3.3268800066450854 75.95811288708757 chr11 135006516 382089968 2.8301594568961397 12.931544068991418 chr12 133851895 367867161 2.7483149267330136 5.879311616127186 chr13 115169878 245280922 2.1297315431731203 5.030555943843703 chr14 107349540 252230143 2.349615499051044 5.835222205332612 chr15 102531392 240024334 2.3409838618010763 5.343151959468165 chr16 90354753 258414096 2.859994493040117 13.65899263659259 chr17 81195210 233033665 2.8700420258781274 13.031016146505008 chr18 78077248 231425054 2.964052395904118 33.74154683351702 chr19 59128983 164217823 2.777281371472261 33.23689077816087 chr20 63025520 187648348 2.977339147697631 8.533793091373289 chr21 48129895 113224657 2.352480864543752 12.119491665354547 chr22 51304566 102980821 2.0072447547845935 5.361293724186929 chrMT 16571 41639658 2512.8029690423027 534.3444069086033 chrX 155270560 224798861 1.4477880481657308 6.735633744889847 chrY 59373566 73350445 1.2354057527890443 23.23315228639237