BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006432.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 1,365,167 number of mapped reads = 1,256,577 (92.05%) number of supplementary alignments = 3,466 (0.25%) number of secondary alignments = 0 number of mapped bases = 71,717,406 bp number of sequenced bases = 71,695,831 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,327 duplication rate = 3.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4707 >>>>>>> ACTG content number of A's = 20,236,857 bp (28.23%) number of C's = 15,187,571 bp (21.18%) number of T's = 20,747,550 bp (28.94%) number of G's = 15,521,164 bp (21.65%) number of N's = 2,689 bp (0%) GC percentage = 42.83% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 297,247 number of insertions = 4,611 mapped reads with insertion percentage = 0.37% number of deletions = 12,846 mapped reads with deletion percentage = 1.02% homopolymer indels = 45.96% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.2151X There is a 2.03% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 5738669 0.023023689878790714 0.24662892494072727 chr2 243199373 6171253 0.025375283348283963 0.20040995833062863 chr3 198022430 5047643 0.025490258856029593 0.17708854316228612 chr4 191154276 4790438 0.025060585095151102 0.18198633269796793 chr5 180915260 4462524 0.024666376954602946 0.17442220497382477 chr6 171115067 4212250 0.024616476350384737 0.18008488849950746 chr7 159138663 4041669 0.025397153173267517 0.21239197123550824 chr8 146364022 3739194 0.02554722088738447 0.42806788128589207 chr9 141213431 3029957 0.02145657802195883 0.18009102675295724 chr10 135534747 3342556 0.02466198575631679 0.20541570499456635 chr11 135006516 3330634 0.024670172215984006 0.18714624261006546 chr12 133851895 3231361 0.024141316788977848 0.17318231855227326 chr13 115169878 2242810 0.01947392876460284 0.1554262139999042 chr14 107349540 2243211 0.020896326151001673 0.3344437889297944 chr15 102531392 2073199 0.02022013901849689 0.15793857160966074 chr16 90354753 2142915 0.02371668261878819 0.18568650138385598 chr17 81195210 1865791 0.022979077214037625 0.1782806887889504 chr18 78077248 1917068 0.024553478114392558 0.23109130186907928 chr19 59128983 1296680 0.021929685480976395 0.20925357799043637 chr20 63025520 1611094 0.025562565767009934 0.19238229239906668 chr21 48129895 1310205 0.027222270067283547 0.19433996662680594 chr22 51304566 870965 0.016976364247969663 0.15643557680762485 chrMT 16571 156403 9.438356164383562 6.202157180103521 chrX 155270560 2233283 0.014383170898591466 0.1357339961123416 chrY 59373566 615634 0.010368823055027553 0.15361901350869292