BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082426.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,759,095 number of mapped reads = 2,454,728 (88.97%) number of supplementary alignments = 19,203 (0.7%) number of secondary alignments = 0 number of mapped bases = 164,515,462 bp number of sequenced bases = 164,456,627 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,102 duplication rate = 2.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.362 >>>>>>> ACTG content number of A's = 46,174,705 bp (28.08%) number of C's = 30,475,959 bp (18.53%) number of T's = 51,383,262 bp (31.24%) number of G's = 36,419,497 bp (22.15%) number of N's = 3,204 bp (0%) GC percentage = 40.68% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,384,862 number of insertions = 13,480 mapped reads with insertion percentage = 0.55% number of deletions = 36,384 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.12% >>>>>>> Coverage mean coverageData = 0.0531X std coverageData = 0.4832X There is a 4.6% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% 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 12929553 0.0518737042584941 0.8574346923842111 chr2 243199373 14169546 0.05826308606478192 0.6230998948786564 chr3 198022430 11139318 0.056252809340840836 0.26545495018070786 chr4 191154276 11085466 0.057992247058077845 0.2778039174078931 chr5 180915260 10276139 0.056800841454723056 0.26994825709480375 chr6 171115067 9813263 0.05734891247186316 0.3438478539920667 chr7 159138663 9086536 0.05709823011394786 0.6652209698241973 chr8 146364022 8549204 0.05841055665988736 0.769172386021723 chr9 141213431 6960700 0.049292053529950704 0.4484574292597464 chr10 135534747 7544384 0.055663836521567416 0.42184957001968953 chr11 135006516 7430725 0.05503975082210106 0.3935391385668098 chr12 133851895 7434372 0.05554177622961558 0.2701316732205456 chr13 115169878 5425940 0.04711249238277391 0.24169500209076805 chr14 107349540 5038527 0.04693571113579061 0.2670596958176559 chr15 102531392 4576114 0.044631345685816885 0.250271182003722 chr16 90354753 4381724 0.04849467077841495 0.2899608372431753 chr17 81195210 4067500 0.050095319662329836 0.28562912999152357 chr18 78077248 4470324 0.057255143009138844 0.8425220100597014 chr19 59128983 2967610 0.05018875430345217 0.6437859536372205 chr20 63025520 3184623 0.05052910313155687 0.26351111570482033 chr21 48129895 2146555 0.044599203883573815 0.2570633349358187 chr22 51304566 1615777 0.031493824545752905 0.19680970133551642 chrMT 16571 4179 0.252187556574739 0.5378166681274672 chrX 155270560 9814594 0.06320962582990619 0.3318682937618534 chrY 59373566 402789 0.006783978580636373 0.12943984450312096