BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082420.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 = 2,851,070 number of mapped reads = 2,540,407 (89.1%) number of supplementary alignments = 18,522 (0.65%) number of secondary alignments = 0 number of mapped bases = 168,559,649 bp number of sequenced bases = 168,498,421 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,436 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6781 >>>>>>> ACTG content number of A's = 46,399,165 bp (27.54%) number of C's = 31,643,395 bp (18.78%) number of T's = 51,952,792 bp (30.83%) number of G's = 38,499,671 bp (22.85%) number of N's = 3,398 bp (0%) GC percentage = 41.63% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,407,662 number of insertions = 13,636 mapped reads with insertion percentage = 0.53% number of deletions = 37,495 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.07% >>>>>>> Coverage mean coverageData = 0.0544X std coverageData = 0.4706X There is a 4.66% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.09% 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 13441131 0.053926168553056486 0.7612032291137769 chr2 243199373 14432884 0.05934589313270968 0.6842160411214065 chr3 198022430 11264203 0.05688347022102496 0.26902251266848354 chr4 191154276 11127614 0.05821273911759107 0.28986744435821665 chr5 180915260 10376863 0.05735758829852164 0.2728071085222292 chr6 171115067 9917326 0.05795705880184122 0.3368641383032495 chr7 159138663 9424797 0.059223804085874465 0.6925495663041461 chr8 146364022 8411168 0.05746745603916241 0.60354878131621 chr9 141213431 7166668 0.050750611675174154 0.4574506452619109 chr10 135534747 7872320 0.05808340793966288 0.41347863449594663 chr11 135006516 7382187 0.054680227434355834 0.40709744761350036 chr12 133851895 7703503 0.05755243883547558 0.2788836295131581 chr13 115169878 5399442 0.04688241486198327 0.2433036972277827 chr14 107349540 5101658 0.04752379935675551 0.2810832970503551 chr15 102531392 4769350 0.04651599775413173 0.2564859239628078 chr16 90354753 4762714 0.05271127242193889 0.3027507689302892 chr17 81195210 4390119 0.054068694446384215 0.29263112629050936 chr18 78077248 4556385 0.058357397535322965 0.8732592585146016 chr19 59128983 3332423 0.05635853740288413 0.6136948714625186 chr20 63025520 3310268 0.0525226606619033 0.27122451404239245 chr21 48129895 2183152 0.04535958368494259 0.26006152693677376 chr22 51304566 1813892 0.035355371683682114 0.21133762113049814 chrMT 16571 10869 0.6559048940920886 0.9982172784346538 chrX 155270560 9966730 0.0641894381008222 0.3382690660257991 chrY 59373566 441983 0.007444103997391701 0.1582720660110591