BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080669.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 = 1,634,706 number of mapped reads = 1,474,668 (90.21%) number of supplementary alignments = 12,869 (0.79%) number of secondary alignments = 0 number of mapped bases = 96,909,764 bp number of sequenced bases = 96,874,049 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,148 duplication rate = 3.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8439 >>>>>>> ACTG content number of A's = 25,807,927 bp (26.64%) number of C's = 18,164,847 bp (18.75%) number of T's = 30,351,681 bp (31.33%) number of G's = 22,544,999 bp (23.27%) number of N's = 4,595 bp (0%) GC percentage = 42.02% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 672,966 number of insertions = 7,319 mapped reads with insertion percentage = 0.49% number of deletions = 22,419 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.79% >>>>>>> Coverage mean coverageData = 0.0313X std coverageData = 0.2696X There is a 2.69% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 11748231 0.04713420954726528 0.31280731154762276 chr2 243199373 6620769 0.02722362692933423 0.4009680959316091 chr3 198022430 6234107 0.03148182253899218 0.19974668689988373 chr4 191154276 3847371 0.020127046490971513 0.16396033770186935 chr5 180915260 4352132 0.02405619072708405 0.17428150958135988 chr6 171115067 5567510 0.0325366438947191 0.24862051534532956 chr7 159138663 6299447 0.039584641979806004 0.5731014869746767 chr8 146364022 11326066 0.07738285574032668 0.3531119308061823 chr9 141213431 3162583 0.022395766306393335 0.20441366969323968 chr10 135534747 4648835 0.034299949665306126 0.22230699943002083 chr11 135006516 4027028 0.029828397319726405 0.20983675189228335 chr12 133851895 3103773 0.0231881139971907 0.17375466399985073 chr13 115169878 1905796 0.016547694875564598 0.14563696901327391 chr14 107349540 1907377 0.01776791032360269 0.15684296970122302 chr15 102531392 1887628 0.018410244542471442 0.1605198489172503 chr16 90354753 2557258 0.02830241813621028 0.1970067699926299 chr17 81195210 1711612 0.02108020904188806 0.16877398786358838 chr18 78077248 3012275 0.03858070151243036 0.29394584413583985 chr19 59128983 1642951 0.027785882940012684 0.2223746143640032 chr20 63025520 2600065 0.04125416180620168 0.23243334394871057 chr21 48129895 1346551 0.027977434814682227 0.19345339972977807 chr22 51304566 1022670 0.019933313537824293 0.15839688226937676 chrMT 16571 13558 0.8181763321465211 1.0754830126521338 chrX 155270560 6162223 0.03968700183730902 0.23504601939118047 chrY 59373566 201948 0.003401311620730343 0.07441834688913292