BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084863.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 = 2,511,090 number of mapped reads = 2,230,914 (88.84%) number of supplementary alignments = 16,080 (0.64%) number of secondary alignments = 0 number of mapped bases = 154,534,205 bp number of sequenced bases = 154,475,875 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,465 duplication rate = 3.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5837 >>>>>>> ACTG content number of A's = 44,969,107 bp (29.11%) number of C's = 28,270,324 bp (18.3%) number of T's = 49,562,054 bp (32.08%) number of G's = 31,650,174 bp (20.49%) number of N's = 24,216 bp (0.02%) GC percentage = 38.79% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,280,129 number of insertions = 12,419 mapped reads with insertion percentage = 0.55% number of deletions = 33,056 mapped reads with deletion percentage = 1.47% homopolymer indels = 48.13% >>>>>>> Coverage mean coverageData = 0.0499X std coverageData = 0.4413X There is a 4.18% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.1% 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% 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 12188893 0.04890215699803613 0.9706458798612981 chr2 243199373 15144459 0.06227178472207657 0.4309996419884535 chr3 198022430 10588353 0.05347047301661736 0.26556269028607327 chr4 191154276 9195162 0.04810335500943751 0.26035519411902563 chr5 180915260 9047398 0.050009037380263 0.26827761007938167 chr6 171115067 8099015 0.047330811611113126 0.2537605715531156 chr7 159138663 7891514 0.049588917307920324 0.3264454746032411 chr8 146364022 9324502 0.06370760978404925 0.7517498644764393 chr9 141213431 10577959 0.074907598555551 0.42465226791429955 chr10 135534747 6373814 0.04702715828288668 0.3439176393761747 chr11 135006516 5206319 0.038563464596034755 0.28153108831638624 chr12 133851895 6171908 0.046109978495261494 0.24920800885859573 chr13 115169878 7938548 0.06892903021048612 0.30172459756338166 chr14 107349540 2724803 0.025382530749549555 0.2010455543996387 chr15 102531392 3770688 0.036775936875995986 0.21755884353912353 chr16 90354753 3592867 0.039764006659395106 0.2578708568864155 chr17 81195210 3667896 0.04517379781393508 0.2515224628528991 chr18 78077248 4447514 0.05696299644167786 0.7162757195875316 chr19 59128983 3331332 0.05634008621457264 0.5364552699233108 chr20 63025520 2926109 0.046427367834489905 0.26105309175499153 chr21 48129895 1665617 0.0346067033805081 0.22429907162750812 chr22 51304566 1407973 0.02744342482109682 0.18689131195059946 chrMT 16571 48193 2.9082734898316334 2.345570135408368 chrX 155270560 8852491 0.05701332564267173 0.29232205237191616 chrY 59373566 350878 0.005909666938313929 0.14778218829944084