BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094042.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 = 418,392 number of mapped reads = 397,797 (95.08%) number of supplementary alignments = 11,963 (2.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 199,790 number of mapped paired reads (second in pair) = 198,007 number of mapped paired reads (both in pair) = 394,972 number of mapped paired reads (singletons) = 2,825 number of mapped bases = 53,363,414 bp number of sequenced bases = 52,085,038 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 373,976 duplication rate = 50.11% >>>>>>> Insert size mean insert size = 472,059.5233 std insert size = 6,250,129.3229 median insert size = 172 >>>>>>> Mapping quality mean mapping quality = 43.8437 >>>>>>> ACTG content number of A's = 14,333,163 bp (27.52%) number of C's = 11,645,965 bp (22.36%) number of T's = 13,923,406 bp (26.73%) number of G's = 12,182,049 bp (23.39%) number of N's = 455 bp (0%) GC percentage = 45.75% >>>>>>> Mismatches and indels general error rate = 0.0438 number of mismatches = 2,210,648 number of insertions = 38,716 mapped reads with insertion percentage = 9.58% number of deletions = 173,891 mapped reads with deletion percentage = 40.62% homopolymer indels = 29.57% >>>>>>> Coverage mean coverageData = 0.0172X std coverageData = 4.4178X 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% 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 638864 0.0025631390503135397 0.8716350079442909 chr2 243199373 1929739 0.007934802529281191 2.2968639290811863 chr3 198022430 922701 0.004659578210407781 1.7420378035662412 chr4 191154276 954220 0.004991884147022691 2.2580791617844844 chr5 180915260 325917 0.0018014898245731178 0.5899387498203131 chr6 171115067 1758336 0.010275752047012903 4.1553140582445005 chr7 159138663 1043495 0.0065571431877619836 2.2896988118496444 chr8 146364022 1057235 0.007223325688603993 2.1057982413323497 chr9 141213431 652658 0.0046217841700907335 1.7434109481685014 chr10 135534747 937813 0.00691935478361132 2.1661123045890345 chr11 135006516 1325544 0.009818370544426167 2.324169654558062 chr12 133851895 1866191 0.01394220828924387 5.016484535322021 chr13 115169878 1540301 0.013374165421969102 4.276620931081981 chr14 107349540 179201 0.0016693224768359511 0.5927993113526281 chr15 102531392 569909 0.005558385474762695 1.7804630434356485 chr16 90354753 431218 0.004772499350421554 1.2965808082084171 chr17 81195210 1408450 0.01734646662038315 4.333549671162663 chr18 78077248 256763 0.003288576462121206 0.9036551246491741 chr19 59128983 230093 0.003891374218291561 1.2909170513559725 chr20 63025520 239274 0.003796462131530212 1.0836181937996903 chr21 48129895 134120 0.0027866256512714188 0.5412418807743006 chr22 51304566 145114 0.0028284811921028626 0.5914079028884921 chrMT 16571 3928787 237.08810572687224 976.9503421051447 chrX 155270560 30598936 0.19706849772423052 13.032968991697052 chrY 59373566 288535 0.004859654210427583 1.6840048364463704