BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089561.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 11,544,476 number of mapped reads = 9,632,059 (83.43%) number of supplementary alignments = 368 (0%) number of secondary alignments = 0 number of mapped bases = 452,058,455 bp number of sequenced bases = 451,969,472 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,331,599 duplication rate = 25.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.488 >>>>>>> ACTG content number of A's = 145,924,895 bp (32.29%) number of C's = 89,036,285 bp (19.7%) number of T's = 113,741,180 bp (25.17%) number of G's = 103,260,200 bp (22.85%) number of N's = 6,912 bp (0%) GC percentage = 42.55% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 2,073,035 number of insertions = 17,964 mapped reads with insertion percentage = 0.19% number of deletions = 58,413 mapped reads with deletion percentage = 0.61% homopolymer indels = 43.89% >>>>>>> Coverage mean coverageData = 0.146X std coverageData = 1.2544X There is a 4.62% of reference with a coverageData >= 1X There is a 2.33% of reference with a coverageData >= 2X There is a 1.52% of reference with a coverageData >= 3X There is a 1.1% of reference with a coverageData >= 4X There is a 0.83% of reference with a coverageData >= 5X There is a 0.65% of reference with a coverageData >= 6X There is a 0.51% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% 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 36742376 0.14741137194599005 1.3511781542493742 chr2 243199373 38156965 0.15689581979308803 1.3357110039320252 chr3 198022430 30660733 0.1548346467619855 1.245266854957219 chr4 191154276 29774891 0.15576366703928715 1.2727992017738532 chr5 180915260 28315586 0.15651297740168518 1.2490513071620548 chr6 171115067 26533983 0.15506514689323062 1.302462884724256 chr7 159138663 25149589 0.1580356936893456 1.3472302335700357 chr8 146364022 22975212 0.15697308454669276 1.42367434530649 chr9 141213431 19202015 0.13597867330339136 1.192651426178045 chr10 135534747 21323845 0.15733120452130256 1.289200723264195 chr11 135006516 20743196 0.15364588772885598 1.288894910186708 chr12 133851895 18796403 0.14042687255193512 1.1724595287880226 chr13 115169878 14788571 0.12840658735437752 1.1501678858685485 chr14 107349540 11349896 0.10572840833784662 1.1245337415103518 chr15 102531392 13149247 0.12824605950926718 1.0996510480992034 chr16 90354753 13488612 0.14928502986444997 1.2336188530011678 chr17 81195210 12671897 0.1560670512460033 1.2312448051220988 chr18 78077248 11902451 0.1524445508120368 1.2598128679243004 chr19 59128983 9220404 0.15593713154173477 1.2792996530125207 chr20 63025520 9674390 0.1534995665247982 1.2249947672071315 chr21 48129895 5859182 0.12173685398648802 1.1691942046941914 chr22 51304566 5320899 0.103711997095931 0.9639807693131034 chrMT 16571 40260 2.429545591696337 7.068968376427861 chrX 155270560 25075458 0.1614952506128657 1.2933569889797638 chrY 59373566 1142394 0.019240784695330578 0.3952315733455718