BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472579.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 8,404,600 number of mapped reads = 7,707,250 (91.7%) number of supplementary alignments = 252,278 (3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,887,004 number of mapped paired reads (second in pair) = 3,820,246 number of mapped paired reads (both in pair) = 7,523,198 number of mapped paired reads (singletons) = 184,052 number of mapped bases = 628,337,052 bp number of sequenced bases = 628,069,397 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,162,109 duplication rate = 12.77% >>>>>>> Insert size mean insert size = 255,247.4665 std insert size = 4,892,314.1673 median insert size = 129 >>>>>>> Mapping quality mean mapping quality = 50.343 >>>>>>> ACTG content number of A's = 161,700,981 bp (25.75%) number of C's = 125,666,671 bp (20.01%) number of T's = 186,867,638 bp (29.75%) number of G's = 153,410,658 bp (24.43%) number of N's = 423,449 bp (0.07%) GC percentage = 44.43% >>>>>>> Mismatches and indels general error rate = 0.0122 number of mismatches = 7,557,427 number of insertions = 61,481 mapped reads with insertion percentage = 0.78% number of deletions = 142,098 mapped reads with deletion percentage = 1.81% homopolymer indels = 42.45% >>>>>>> Coverage mean coverageData = 0.203X std coverageData = 2.1389X There is a 11.27% of reference with a coverageData >= 1X There is a 5% of reference with a coverageData >= 2X There is a 1.72% of reference with a coverageData >= 3X There is a 0.81% of reference with a coverageData >= 4X There is a 0.37% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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% 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 39260276 0.1575132524945645 2.5456753398308702 chr2 243199373 63284967 0.2602184628165139 3.1398418287734633 chr3 198022430 32306232 0.1631443064303372 0.6035697799480096 chr4 191154276 31444324 0.16449709971436893 1.1726825537769885 chr5 180915260 30941844 0.17102948640153406 0.6784579347404104 chr6 171115067 42550092 0.24866362001891978 1.175637779291048 chr7 159138663 53425986 0.33571971130610795 3.953595437433058 chr8 146364022 32204534 0.22003039790748577 1.8226481185305754 chr9 141213431 22228694 0.15741203823593805 2.420203999638849 chr10 135534747 25138800 0.1854786359692692 1.8575505589191679 chr11 135006516 22333491 0.16542528213971538 1.6228605282425346 chr12 133851895 31493889 0.23528907827565684 0.8009507697090793 chr13 115169878 30800746 0.267437515215567 0.8246677773281204 chr14 107349540 16384834 0.15263068663358967 4.587030788846173 chr15 102531392 14629420 0.1426823503966473 0.5737151445891843 chr16 90354753 23011911 0.2546840120297822 1.1557275180548257 chr17 81195210 23159365 0.28523068047979677 1.9006042942554038 chr18 78077248 14256824 0.18259895635665846 4.298793689052028 chr19 59128983 12365242 0.2091231976710981 1.7946120720255285 chr20 63025520 20136155 0.31949208828423786 1.1998219307466513 chr21 48129895 9209479 0.19134633474683457 0.8609359784602666 chr22 51304566 6532314 0.12732422295512644 0.54736450654045 chrMT 16571 174671 10.54076398527548 7.9410065881259255 chrX 155270560 29614826 0.19073046429406837 1.0202692516332883 chrY 59373566 1448136 0.02439024801036879 0.9197556546798834