BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818758.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,581,538 number of mapped reads = 3,484,854 (97.3%) number of supplementary alignments = 24,607 (0.69%) number of secondary alignments = 0 number of mapped bases = 237,061,267 bp number of sequenced bases = 236,963,640 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,940,110 duplication rate = 46.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4841 >>>>>>> ACTG content number of A's = 68,430,688 bp (28.88%) number of C's = 49,920,635 bp (21.07%) number of T's = 69,118,714 bp (29.17%) number of G's = 49,479,197 bp (20.88%) number of N's = 14,406 bp (0.01%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,215,172 number of insertions = 28,870 mapped reads with insertion percentage = 0.82% number of deletions = 59,764 mapped reads with deletion percentage = 1.7% homopolymer indels = 40.54% >>>>>>> Coverage mean coverageData = 0.0766X std coverageData = 0.9142X There is a 2.76% of reference with a coverageData >= 1X There is a 1.59% of reference with a coverageData >= 2X There is a 1.04% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% 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% 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 19543637 0.07840958197652795 1.427888010115896 chr2 243199373 20721308 0.085202966374424 1.4850387705730397 chr3 198022430 16020428 0.08090208770794298 0.6164743360742402 chr4 191154276 15675032 0.0820019950796183 0.7201897398995082 chr5 180915260 14573360 0.08055351439121276 0.6352741543666358 chr6 171115067 14094074 0.08236606072801292 0.7093496293683125 chr7 159138663 12935840 0.08128659469760657 0.8117516200825969 chr8 146364022 12524593 0.08557152795377541 0.7791466713644575 chr9 141213431 10170632 0.07202312080357286 0.7461653905540858 chr10 135534747 11429564 0.08432940078458256 0.9467576001302604 chr11 135006516 11189118 0.08287835529360672 0.7336033953351001 chr12 133851895 10923878 0.08161167983464111 0.8051975697913679 chr13 115169878 7627515 0.0662283848212464 0.5622243345432483 chr14 107349540 7289468 0.06790404504760802 0.6558171235529912 chr15 102531392 6883031 0.06713096219351045 0.5666987173086205 chr16 90354753 7072671 0.0782766901039506 1.0142798296029911 chr17 81195210 6312597 0.07774592860835017 0.6555627486582378 chr18 78077248 6341515 0.08122103637669197 1.005801588403761 chr19 59128983 4627859 0.07826718413201864 1.139739933048426 chr20 63025520 5029672 0.07980373664509234 0.6646700020452609 chr21 48129895 3205232 0.06659544966802858 0.596725631095629 chr22 51304566 2894105 0.056410281299329186 0.5735994985438532 chrMT 16571 310387 18.73073441554523 16.97062743121071 chrX 155270560 7489221 0.04823336117291005 0.571657198716331 chrY 59373566 2176530 0.036658232722622724 1.4988340119671912