BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777269.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 = 56,564,284 number of mapped reads = 56,128,483 (99.23%) number of supplementary alignments = 2,044,951 (3.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 28,067,779 number of mapped paired reads (second in pair) = 28,060,704 number of mapped paired reads (both in pair) = 55,948,990 number of mapped paired reads (singletons) = 179,493 number of mapped bases = 5,626,923,018 bp number of sequenced bases = 5,626,078,074 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,586,000 duplication rate = 37.32% >>>>>>> Insert size mean insert size = 338,640.8546 std insert size = 5,695,311.9711 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 54.5707 >>>>>>> ACTG content number of A's = 1,564,733,861 bp (27.81%) number of C's = 1,248,669,496 bp (22.19%) number of T's = 1,553,058,320 bp (27.6%) number of G's = 1,259,378,635 bp (22.38%) number of N's = 237,762 bp (0%) GC percentage = 44.58% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 13,868,444 number of insertions = 1,015,132 mapped reads with insertion percentage = 1.78% number of deletions = 371,158 mapped reads with deletion percentage = 0.65% homopolymer indels = 51.89% >>>>>>> Coverage mean coverageData = 1.8177X std coverageData = 16.2413X There is a 22.44% of reference with a coverageData >= 1X There is a 11.39% of reference with a coverageData >= 2X There is a 6.7% of reference with a coverageData >= 3X There is a 4.83% of reference with a coverageData >= 4X There is a 3.82% of reference with a coverageData >= 5X There is a 3.28% of reference with a coverageData >= 6X There is a 2.92% of reference with a coverageData >= 7X There is a 2.68% of reference with a coverageData >= 8X There is a 2.49% of reference with a coverageData >= 9X There is a 2.34% of reference with a coverageData >= 10X There is a 2.22% of reference with a coverageData >= 11X There is a 2.12% of reference with a coverageData >= 12X There is a 2.02% of reference with a coverageData >= 13X There is a 1.94% of reference with a coverageData >= 14X There is a 1.87% of reference with a coverageData >= 15X There is a 1.8% of reference with a coverageData >= 16X There is a 1.74% of reference with a coverageData >= 17X There is a 1.68% of reference with a coverageData >= 18X There is a 1.63% of reference with a coverageData >= 19X There is a 1.58% of reference with a coverageData >= 20X There is a 1.53% of reference with a coverageData >= 21X There is a 1.49% of reference with a coverageData >= 22X There is a 1.44% of reference with a coverageData >= 23X There is a 1.41% of reference with a coverageData >= 24X There is a 1.37% of reference with a coverageData >= 25X There is a 1.33% of reference with a coverageData >= 26X There is a 1.3% of reference with a coverageData >= 27X There is a 1.27% of reference with a coverageData >= 28X There is a 1.24% of reference with a coverageData >= 29X There is a 1.21% of reference with a coverageData >= 30X There is a 1.18% of reference with a coverageData >= 31X There is a 1.15% of reference with a coverageData >= 32X There is a 1.12% of reference with a coverageData >= 33X There is a 1.1% of reference with a coverageData >= 34X There is a 1.08% of reference with a coverageData >= 35X There is a 1.05% of reference with a coverageData >= 36X There is a 1.03% of reference with a coverageData >= 37X There is a 1.01% of reference with a coverageData >= 38X There is a 0.99% of reference with a coverageData >= 39X There is a 0.97% of reference with a coverageData >= 40X There is a 0.95% of reference with a coverageData >= 41X There is a 0.93% of reference with a coverageData >= 42X There is a 0.91% of reference with a coverageData >= 43X There is a 0.89% of reference with a coverageData >= 44X There is a 0.88% of reference with a coverageData >= 45X There is a 0.86% of reference with a coverageData >= 46X There is a 0.84% of reference with a coverageData >= 47X There is a 0.83% of reference with a coverageData >= 48X There is a 0.81% of reference with a coverageData >= 49X There is a 0.8% of reference with a coverageData >= 50X There is a 0.78% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 554147977 2.2232561538933937 18.25334418528573 chr2 243199373 499338808 2.0532076289522343 16.732469735668204 chr3 198022430 349567494 1.7652924166216928 16.380514135319082 chr4 191154276 252427687 1.3205442864380392 12.626279879832992 chr5 180915260 297061026 1.6419898796817913 14.36554882921398 chr6 171115067 264630401 1.5465055511447159 13.670286703593982 chr7 159138663 373420685 2.346511387996266 20.360312709950204 chr8 146364022 192762688 1.317008684005691 13.812799163900214 chr9 141213431 193590713 1.3709086425355672 13.21518522256761 chr10 135534747 236277905 1.7433013321668722 14.764921548911058 chr11 135006516 383578052 2.841181769330304 22.5682611279683 chr12 133851895 321849049 2.4045161930654775 18.208742611755536 chr13 115169878 168410541 1.462279407815297 14.761348859349052 chr14 107349540 123640171 1.1517531514340908 11.529936280406552 chr15 102531392 265212745 2.5866492186119934 21.471207377291705 chr16 90354753 160124127 1.7721715978793058 14.25253816213372 chr17 81195210 237959162 2.9307044344118327 21.92583228697569 chr18 78077248 87915010 1.1260003682506843 11.044981895431643 chr19 59128983 264125884 4.466944476281623 28.66023302028384 chr20 63025520 152390786 2.417921914805304 18.40927635113165 chr21 48129895 37409111 0.7772531188775708 9.781517611997376 chr22 51304566 55543010 1.0826133876661193 9.620651121727802 chrMT 16571 2344059 141.45549453865186 47.70619062854166 chrX 155270560 151370652 0.9748831459099523 10.321840709360533 chrY 59373566 1825275 0.030742216157271067 0.9063606605167659