BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081169.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 = 1,798,239 number of mapped reads = 1,506,092 (83.75%) number of supplementary alignments = 13,384 (0.74%) number of secondary alignments = 0 number of mapped bases = 98,623,526 bp number of sequenced bases = 98,588,472 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,588 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.308 >>>>>>> ACTG content number of A's = 27,059,102 bp (27.45%) number of C's = 17,895,210 bp (18.15%) number of T's = 31,383,655 bp (31.83%) number of G's = 22,222,078 bp (22.54%) number of N's = 28,427 bp (0.03%) GC percentage = 40.69% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 845,166 number of insertions = 7,339 mapped reads with insertion percentage = 0.48% number of deletions = 21,987 mapped reads with deletion percentage = 1.45% homopolymer indels = 46.81% >>>>>>> Coverage mean coverageData = 0.0319X std coverageData = 0.2716X There is a 2.81% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7626224 0.0305966098275037 0.4070663797115194 chr2 243199373 8201469 0.03372323250191932 0.3491732523223558 chr3 198022430 6767226 0.034174037759257876 0.20304058425771856 chr4 191154276 6944182 0.0363276309863976 0.21578073472678505 chr5 180915260 5669207 0.03133625654353314 0.1953427015036822 chr6 171115067 5797753 0.03388218876132047 0.2660332551241835 chr7 159138663 5310729 0.03337170804306682 0.33144330458327953 chr8 146364022 5577969 0.03811024679275348 0.3614336622524667 chr9 141213431 3605679 0.025533541494363945 0.23515008834000176 chr10 135534747 4253984 0.031386667213832625 0.23802073430765178 chr11 135006516 4631295 0.03430423313790277 0.2604060452730136 chr12 133851895 5331054 0.039828005423457026 0.22141047754954246 chr13 115169878 3185976 0.02766327494069239 0.1835203524066014 chr14 107349540 3023905 0.028168774640301205 0.19271356393411276 chr15 102531392 2919731 0.028476459190176606 0.19116991922118617 chr16 90354753 2452945 0.02714793542737038 0.1935907096007307 chr17 81195210 2373332 0.029229950880107335 0.21477588728040745 chr18 78077248 2714956 0.034772690758772644 0.4341645175050773 chr19 59128983 1719390 0.02907863306223278 0.2980012314773999 chr20 63025520 1827167 0.028990907175379117 0.19383954389069852 chr21 48129895 1407697 0.02924787182685522 0.19564471579633907 chr22 51304566 1076640 0.020985266691467577 0.15843675278419822 chrMT 16571 1343 0.08104519944481323 0.29602768068937746 chrX 155270560 5953762 0.03834443567409044 0.2381622280337582 chrY 59373566 249911 0.004209129025533012 0.0856541085546661