BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082443.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 = 2,553,991 number of mapped reads = 2,307,939 (90.37%) number of supplementary alignments = 18,889 (0.74%) number of secondary alignments = 0 number of mapped bases = 155,848,804 bp number of sequenced bases = 155,792,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,381 duplication rate = 2.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7237 >>>>>>> ACTG content number of A's = 43,872,883 bp (28.16%) number of C's = 29,269,774 bp (18.79%) number of T's = 48,335,476 bp (31.03%) number of G's = 34,311,459 bp (22.02%) number of N's = 3,219 bp (0%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,291,550 number of insertions = 12,507 mapped reads with insertion percentage = 0.54% number of deletions = 34,655 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.05% >>>>>>> Coverage mean coverageData = 0.0503X std coverageData = 0.4196X There is a 4.39% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.07% 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 12313158 0.04940071142290153 0.6916550108501563 chr2 243199373 13309593 0.05472708599458437 0.5392076634088768 chr3 198022430 10617287 0.05361658777745531 0.2565567992568777 chr4 191154276 10553656 0.05521014868639402 0.26987964449655255 chr5 180915260 9382598 0.05186183852042111 0.2541648147194453 chr6 171115067 9294561 0.054317607227422 0.3093055025151763 chr7 159138663 8642596 0.054308587473805785 0.5866030570679149 chr8 146364022 8074115 0.05516461552279562 0.681579014844216 chr9 141213431 6571643 0.04653695440627032 0.38170523163615266 chr10 135534747 7207343 0.053177086758423656 0.3725353163087854 chr11 135006516 7072214 0.05238424195762521 0.3616917204815898 chr12 133851895 7048675 0.05266025557576155 0.25905665266092054 chr13 115169878 5177303 0.04495362059860826 0.2346850762593762 chr14 107349540 4758506 0.044327213698354 0.2544433304300917 chr15 102531392 4445049 0.04335305425288676 0.23967696595775045 chr16 90354753 4249441 0.04703063047496793 0.2769185913256768 chr17 81195210 3963077 0.048809246259723944 0.2744910146846291 chr18 78077248 4299429 0.055066349162306544 0.7068340343178556 chr19 59128983 2795784 0.047282802073561794 0.5206503803939265 chr20 63025520 2947047 0.04675958246754648 0.25087804912596323 chr21 48129895 2047791 0.042547173643325005 0.24555983002118326 chr22 51304566 1570003 0.03060162325513094 0.19295339779726528 chrMT 16571 7897 0.47655542815762475 0.7645217457461493 chrX 155270560 9119649 0.058733922258024956 0.30098781884881604 chrY 59373566 380389 0.006406706311020632 0.13072354822144044