BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081941.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 = 3,119,322 number of mapped reads = 2,897,107 (92.88%) number of supplementary alignments = 21,206 (0.68%) number of secondary alignments = 0 number of mapped bases = 199,859,308 bp number of sequenced bases = 199,787,739 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 143,152 duplication rate = 4.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5313 >>>>>>> ACTG content number of A's = 57,754,743 bp (28.91%) number of C's = 36,414,504 bp (18.23%) number of T's = 64,141,752 bp (32.1%) number of G's = 41,450,732 bp (20.75%) number of N's = 26,008 bp (0.01%) GC percentage = 38.97% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,449,012 number of insertions = 14,048 mapped reads with insertion percentage = 0.48% number of deletions = 40,737 mapped reads with deletion percentage = 1.39% homopolymer indels = 48.88% >>>>>>> Coverage mean coverageData = 0.0646X std coverageData = 0.4575X There is a 5.28% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% 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 18374055 0.07371718845185947 0.7116229743733071 chr2 243199373 17615950 0.07243419167861095 0.5506782314065368 chr3 198022430 12712794 0.06419875768618737 0.2977736117942811 chr4 191154276 10499276 0.054925666428722736 0.2846580597485535 chr5 180915260 10316560 0.05702426649913335 0.27957468268900915 chr6 171115067 17971115 0.10502356873109252 0.4825248982870206 chr7 159138663 13039326 0.0819368829308312 0.5238288401587063 chr8 146364022 11731990 0.08015624222187609 0.8297397233459549 chr9 141213431 9616532 0.06809927307835187 0.4625706984063056 chr10 135534747 8034320 0.05927867338698024 0.4516477300108049 chr11 135006516 8903253 0.0659468391881174 0.35675893284502486 chr12 133851895 8692096 0.0649381616898289 0.3040264654707354 chr13 115169878 5436495 0.04720413961018523 0.2539299476695379 chr14 107349540 5084127 0.047360491717058126 0.2690076316162833 chr15 102531392 4492882 0.04381957478934842 0.24422370515270575 chr16 90354753 4000368 0.04427401843486861 0.27986291888907305 chr17 81195210 5089215 0.06267875900561129 0.3173269919770155 chr18 78077248 5846969 0.07488697603686031 0.7524628929938667 chr19 59128983 3658737 0.0618772184869136 0.5261145941671884 chr20 63025520 4862850 0.07715684059409585 0.3307868904663432 chr21 48129895 2197402 0.04565565746611332 0.2688061856638419 chr22 51304566 1401105 0.027309557593762707 0.1877179594311309 chrMT 16571 92106 5.558264437873393 3.5884303687974133 chrX 155270560 9791851 0.06306315247397833 0.33210865107892 chrY 59373566 397934 0.0067022081846995684 0.14142240524953262