BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708639.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,889,835 number of mapped reads = 4,640,691 (94.9%) number of supplementary alignments = 183 (0%) number of secondary alignments = 0 number of mapped bases = 231,380,057 bp number of sequenced bases = 231,356,988 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,597 duplication rate = 1.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8572 >>>>>>> ACTG content number of A's = 71,630,543 bp (30.96%) number of C's = 43,830,232 bp (18.94%) number of T's = 71,632,896 bp (30.96%) number of G's = 44,255,423 bp (19.13%) number of N's = 7,894 bp (0%) GC percentage = 38.07% >>>>>>> Mismatches and indels general error rate = 0.0018 number of mismatches = 387,609 number of insertions = 16,787 mapped reads with insertion percentage = 0.36% number of deletions = 13,463 mapped reads with deletion percentage = 0.29% homopolymer indels = 49.24% >>>>>>> Coverage mean coverageData = 0.0747X std coverageData = 0.4253X There is a 4.96% of reference with a coverageData >= 1X There is a 1.27% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 16293781 0.06537107484277843 0.3759008280576751 chr2 243199373 21263709 0.08743323939408347 0.4567646333274462 chr3 198022430 13396902 0.06765345723714228 0.34074053172249313 chr4 191154276 14462484 0.07565869988699599 0.38411753934869486 chr5 180915260 10329433 0.05709542135914903 0.322661925397579 chr6 171115067 25966743 0.15175018457024594 0.6970407237984031 chr7 159138663 9005561 0.056589397134749087 0.35595115127515115 chr8 146364022 15734715 0.1075039807255365 0.605487116764973 chr9 141213431 10438674 0.07392125469991591 0.38416198919031164 chr10 135534747 11180664 0.0824929713411425 0.40319157992955373 chr11 135006516 8897168 0.06590176728951364 0.34159097547651496 chr12 133851895 6568181 0.0490705118519241 0.3061182733039627 chr13 115169878 6186519 0.053716467425623214 0.3269412576617672 chr14 107349540 4649471 0.043311513025579805 0.25820123245324256 chr15 102531392 7290634 0.07110635930896168 0.4378450603826426 chr16 90354753 8468260 0.09372235238139603 0.49417588225248954 chr17 81195210 4744913 0.05843833644866489 0.38033369624943547 chr18 78077248 7415535 0.09497690031287988 0.441866859736694 chr19 59128983 2523888 0.042684447997355206 0.27588706528077395 chr20 63025520 17629631 0.27972210304651196 0.9922997343997748 chr21 48129895 2096375 0.04355660863170385 0.27872880502603886 chr22 51304566 1371472 0.026731967677106946 0.23963757927744306 chrMT 16571 200 0.012069277653732424 0.10919528465391506 chrX 155270560 4484144 0.028879550637287584 0.22045522312030222 chrY 59373566 981000 0.016522504307725092 0.17538616132687615