BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093986.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 388,532 number of mapped reads = 371,589 (95.64%) number of supplementary alignments = 22,750 (5.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 186,867 number of mapped paired reads (second in pair) = 184,722 number of mapped paired reads (both in pair) = 368,074 number of mapped paired reads (singletons) = 3,515 number of mapped bases = 48,310,084 bp number of sequenced bases = 47,452,921 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 349,944 duplication rate = 50.08% >>>>>>> Insert size mean insert size = 1,106,485.5523 std insert size = 9,490,894.5838 median insert size = 167 >>>>>>> Mapping quality mean mapping quality = 41.481 >>>>>>> ACTG content number of A's = 12,472,871 bp (26.28%) number of C's = 11,208,622 bp (23.62%) number of T's = 11,807,309 bp (24.88%) number of G's = 11,963,663 bp (25.21%) number of N's = 456 bp (0%) GC percentage = 48.83% >>>>>>> Mismatches and indels general error rate = 0.0351 number of mismatches = 1,612,105 number of insertions = 25,450 mapped reads with insertion percentage = 6.74% number of deletions = 125,154 mapped reads with deletion percentage = 32.32% homopolymer indels = 28.83% >>>>>>> Coverage mean coverageData = 0.0156X std coverageData = 3.0468X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 0.01% 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% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 877911 0.003522201856419848 1.1583401425729636 chr2 243199373 2543934 0.010460281902124806 3.23035872220778 chr3 198022430 762027 0.0038481852788090722 1.2105196858294733 chr4 191154276 1197356 0.006263820119828237 2.318365173523221 chr5 180915260 460647 0.0025462031229427523 1.2176174380864038 chr6 171115067 853479 0.004987748974787825 1.4182440763821673 chr7 159138663 966783 0.0060750981676904 1.8004694865908348 chr8 146364022 520431 0.0035557303829762206 1.092604388698596 chr9 141213431 598681 0.004239547157522148 1.2225037288938703 chr10 135534747 749975 0.0055334518756286165 1.6669540552050803 chr11 135006516 1065381 0.007891330222905685 2.0627556725212575 chr12 133851895 1064111 0.007949913596665926 2.010519872415915 chr13 115169878 956356 0.008303872649756561 2.191950465134192 chr14 107349540 157986 0.001471697037546691 0.545733196645838 chr15 102531392 707666 0.006901944723426753 1.9040977164961814 chr16 90354753 259138 0.0028680062907149996 0.6866437641902333 chr17 81195210 1204120 0.014829938859693817 3.6084536011770054 chr18 78077248 231563 0.002965819184610605 0.8382176059850749 chr19 59128983 162752 0.002752491109140166 0.7363476261715446 chr20 63025520 372345 0.005907844949157103 1.9797423198112554 chr21 48129895 96899 0.0020132809348534834 0.3891030708719332 chr22 51304566 159955 0.0031177536907728643 0.7980190943277706 chrMT 16571 1210306 73.03759579989138 317.66835431115004 chrX 155270560 30563326 0.19683915611562167 10.540056837914221 chrY 59373566 566956 0.009548963254118845 1.2643064735444594