BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084772.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 = 2,710,993 number of mapped reads = 2,431,651 (89.7%) number of supplementary alignments = 20,754 (0.77%) number of secondary alignments = 0 number of mapped bases = 163,671,966 bp number of sequenced bases = 163,602,680 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,549 duplication rate = 3.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6231 >>>>>>> ACTG content number of A's = 44,665,678 bp (27.3%) number of C's = 30,881,227 bp (18.88%) number of T's = 51,091,443 bp (31.23%) number of G's = 36,900,684 bp (22.56%) number of N's = 63,648 bp (0.04%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,447,754 number of insertions = 12,541 mapped reads with insertion percentage = 0.51% number of deletions = 42,219 mapped reads with deletion percentage = 1.72% homopolymer indels = 46.48% >>>>>>> Coverage mean coverageData = 0.0529X std coverageData = 0.4286X There is a 4.48% of reference with a coverageData >= 1X There is a 0.59% 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 12611010 0.05059570142455132 0.6888395559482028 chr2 243199373 14078008 0.057886695291767876 0.5501478571176728 chr3 198022430 10995536 0.05552671987713715 0.2663174920563004 chr4 191154276 10370247 0.054250667141759364 0.2857555633344914 chr5 180915260 9602417 0.05307687698649633 0.2647848926270124 chr6 171115067 9795379 0.05724439800499859 0.35239193488598886 chr7 159138663 9240292 0.05806440638501531 0.6040193659715846 chr8 146364022 8542730 0.058366324478292896 0.43148185678066114 chr9 141213431 6903017 0.04888357255479474 0.4332278290831911 chr10 135534747 7633375 0.05632042829577864 0.39817590538300673 chr11 135006516 7365490 0.05455655192227907 0.40287414988162384 chr12 133851895 7329703 0.054759800001337296 0.2713199183444784 chr13 115169878 5269560 0.04575467206798639 0.2452928314914828 chr14 107349540 4968803 0.04628620672245079 0.2719140059681067 chr15 102531392 4770256 0.046524834072281 0.25868261762440803 chr16 90354753 4729046 0.052338652289824754 0.2999634902318334 chr17 81195210 4267238 0.05255529236268987 0.3176811047715087 chr18 78077248 4578809 0.05864460028099351 0.8974504853802809 chr19 59128983 3108134 0.05256532147694812 0.5447200056139583 chr20 63025520 3456089 0.054836342484758556 0.28152445559824557 chr21 48129895 2187951 0.04545929302359791 0.2614894892335 chr22 51304566 1835004 0.0357668750184925 0.21360945259387318 chrMT 16571 4915 0.2966024983404743 0.6460676521224523 chrX 155270560 9634375 0.06204894862232738 0.3364641941112912 chrY 59373566 394582 0.006645752084353499 0.14264477712865886