BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504420.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,164,713 number of mapped reads = 1,892,118 (87.41%) number of secondary alignments = 0 number of mapped bases = 60,541,356 bp number of sequenced bases = 60,541,356 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 175,591 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.5226 >>>>>>> ACTG content number of A's = 17,295,398 bp (28.57%) number of C's = 12,267,947 bp (20.26%) number of T's = 18,607,755 bp (30.74%) number of G's = 12,370,118 bp (20.43%) number of N's = 138 bp (0%) GC percentage = 40.7% >>>>>>> Mismatches and indels general error rate = 0.0005 number of mismatches = 31,805 >>>>>>> Coverage mean coverageData = 0.0196X std coverageData = 0.7203X There is a 1.45% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 4295810 0.017234901894186253 0.18148565192413077 chr2 243199373 4546766 0.018695632081255405 0.16917854067169033 chr3 198022430 4369264 0.02206449037111604 0.21575746614700175 chr4 191154276 3667768 0.019187475565547903 0.2025802342079729 chr5 180915260 3974992 0.021971568346418096 0.2026200235207783 chr6 171115067 3537426 0.020672790900406215 0.2167616396299075 chr7 159138663 3129016 0.019662198619828798 0.6943235488482674 chr8 146364022 3174182 0.021686900623706554 0.22548455822578914 chr9 141213431 5461964 0.0386787854478233 2.989088720317553 chr10 135534747 3913486 0.02887441107629765 1.1257610142976089 chr11 135006516 2712376 0.0200907043627435 0.18771986299503707 chr12 133851895 2500432 0.01868058722665077 0.16947875508577298 chr13 115169878 1534042 0.013319819614639168 0.14281255890863948 chr14 107349540 1644478 0.015318910542141122 0.1618354905527649 chr15 102531392 1367018 0.013332677664222095 0.1446295635154056 chr16 90354753 1151494 0.012744144184645163 0.13380722304134898 chr17 81195210 1048126 0.012908717152157129 0.13687161710589846 chr18 78077248 1458182 0.01867614493789535 0.19648476567183512 chr19 59128983 755008 0.012768831150030096 0.15520704213138914 chr20 63025520 873322 0.013856640928944338 0.1511041901573535 chr21 48129895 640454 0.013306781575151992 0.16187815506372974 chr22 51304566 338022 0.0065885363887494925 0.09597462218800441 chrMT 16571 32 0.001931084424597188 0.04390165529387549 chrX 155270560 4295530 0.027664806515800548 0.2964613411929959 chrY 59373566 152166 0.002562857686533431 0.05536031868939554