BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084852.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 = 2,245,565 number of mapped reads = 2,019,389 (89.93%) number of supplementary alignments = 24,834 (1.11%) number of secondary alignments = 0 number of mapped bases = 134,866,542 bp number of sequenced bases = 134,813,436 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,366 duplication rate = 4.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4394 >>>>>>> ACTG content number of A's = 36,667,775 bp (27.2%) number of C's = 25,267,061 bp (18.74%) number of T's = 42,385,183 bp (31.44%) number of G's = 30,474,893 bp (22.61%) number of N's = 18,524 bp (0.01%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,055,882 number of insertions = 10,895 mapped reads with insertion percentage = 0.54% number of deletions = 32,247 mapped reads with deletion percentage = 1.58% homopolymer indels = 47.44% >>>>>>> Coverage mean coverageData = 0.0436X std coverageData = 0.3422X There is a 3.61% of reference with a coverageData >= 1X There is a 0.56% 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 11509830 0.04617773851002763 0.5558203875686577 chr2 243199373 11440246 0.04704060647393199 0.5530518090191034 chr3 198022430 10353228 0.052283107524738484 0.2692804899095391 chr4 191154276 6927124 0.03623839416493095 0.22513020935328726 chr5 180915260 7768355 0.04293919153088579 0.24408006874281193 chr6 171115067 7831103 0.04576512832736114 0.2719741679183466 chr7 159138663 7442530 0.04676757903891652 0.32209744314178856 chr8 146364022 7493915 0.05120052658842622 0.3760683885466898 chr9 141213431 9249432 0.06549966199744839 0.39033471366860495 chr10 135534747 4367986 0.03222779469238246 0.22815145941187634 chr11 135006516 4915883 0.036412190653079296 0.25697982999727603 chr12 133851895 5678940 0.04242704221707134 0.24407419972051994 chr13 115169878 3745032 0.03251746085899301 0.2104954880492192 chr14 107349540 2924557 0.027243311894955487 0.20478126946958988 chr15 102531392 3186027 0.031073673514546648 0.21225988082054084 chr16 90354753 2501663 0.027687121229804035 0.20601095487388746 chr17 81195210 4965031 0.06114930917722856 0.2940575577875025 chr18 78077248 5876635 0.07526693307632974 0.5757504867800568 chr19 59128983 3006941 0.05085392725256242 0.373869125550142 chr20 63025520 2786163 0.04420690221992615 0.2559831606843749 chr21 48129895 1194908 0.024826731909554343 0.1949611333263143 chr22 51304566 1277829 0.024906730523751044 0.18084703653581158 chrMT 16571 61268 3.697302516444391 2.8771354584986195 chrX 155270560 8049186 0.05183974347744994 0.2823398914406576 chrY 59373566 312730 0.005267158789148693 0.11946857231829205