BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926965.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 19,902,012 number of mapped reads = 19,299,636 (96.97%) number of supplementary alignments = 666,323 (3.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,702,324 number of mapped paired reads (second in pair) = 9,597,312 number of mapped paired reads (both in pair) = 18,975,400 number of mapped paired reads (singletons) = 324,236 number of mapped bases = 1,705,953,437 bp number of sequenced bases = 1,704,585,970 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,070,874 duplication rate = 8.8% >>>>>>> Insert size mean insert size = 348,089.8982 std insert size = 5,766,455.1715 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 52.4189 >>>>>>> ACTG content number of A's = 484,420,022 bp (28.42%) number of C's = 326,508,061 bp (19.15%) number of T's = 502,966,907 bp (29.51%) number of G's = 390,565,930 bp (22.91%) number of N's = 125,050 bp (0.01%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 17,067,890 number of insertions = 303,481 mapped reads with insertion percentage = 1.54% number of deletions = 922,526 mapped reads with deletion percentage = 4.66% homopolymer indels = 51.51% >>>>>>> Coverage mean coverageData = 0.5511X std coverageData = 2.1368X There is a 26.38% of reference with a coverageData >= 1X There is a 12.77% of reference with a coverageData >= 2X There is a 6.23% of reference with a coverageData >= 3X There is a 3.43% of reference with a coverageData >= 4X There is a 1.96% of reference with a coverageData >= 5X There is a 1.19% of reference with a coverageData >= 6X There is a 0.75% of reference with a coverageData >= 7X There is a 0.49% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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% 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 139840541 0.5610439020731668 2.233929977119981 chr2 243199373 142823895 0.5872708191562649 3.960146389986053 chr3 198022430 111223660 0.5616720287696702 1.290895095296994 chr4 191154276 107894203 0.5644352052056633 1.82492371485424 chr5 180915260 105396693 0.5825749193296353 1.3164905826882867 chr6 171115067 94281972 0.5509857995146623 1.4507199803363193 chr7 159138663 89683215 0.5635539051877041 1.9192405258581977 chr8 146364022 93357329 0.6378434243901825 1.626436780218672 chr9 141213431 73059318 0.5173680540344636 2.595768107843572 chr10 135534747 83146557 0.6134704113919953 2.932156840386418 chr11 135006516 81769545 0.6056710996082589 2.671005876122891 chr12 133851895 76714008 0.5731260509983814 1.5980547977515407 chr13 115169878 54673225 0.47471809425725014 1.2425226528901794 chr14 107349540 52620082 0.49017519776982743 1.3123750177969262 chr15 102531392 50715606 0.49463491142303034 1.3272783649560935 chr16 90354753 47851825 0.5295994224011658 2.6234802293954993 chr17 81195210 43901872 0.5406953439741088 1.5611429169621325 chr18 78077248 45900166 0.587881452993835 2.7155658329592285 chr19 59128983 26301971 0.44482366625517644 1.5100814155752296 chr20 63025520 38518635 0.6111593367258216 1.4614108559420493 chr21 48129895 22376946 0.4649282114577645 1.7643231354137123 chr22 51304566 20015422 0.3901294477376536 1.1861921202012338 chrMT 16571 93075 5.616740088105727 5.114270167383008 chrX 155270560 100575056 0.6477406663568419 1.6265671009381695 chrY 59373566 3218620 0.05420964609065253 1.7254736360030962