BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926933.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 = 8,330,990 number of mapped reads = 8,062,629 (96.78%) number of supplementary alignments = 305,638 (3.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,042,321 number of mapped paired reads (second in pair) = 4,020,308 number of mapped paired reads (both in pair) = 7,941,456 number of mapped paired reads (singletons) = 121,173 number of mapped bases = 731,993,432 bp number of sequenced bases = 731,419,355 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 449,215 duplication rate = 4.63% >>>>>>> Insert size mean insert size = 375,739.5177 std insert size = 5,977,625.5107 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 52.3604 >>>>>>> ACTG content number of A's = 208,976,998 bp (28.57%) number of C's = 142,319,926 bp (19.46%) number of T's = 212,768,791 bp (29.09%) number of G's = 167,217,093 bp (22.86%) number of N's = 136,547 bp (0.02%) GC percentage = 42.32% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 6,984,564 number of insertions = 128,676 mapped reads with insertion percentage = 1.57% number of deletions = 389,446 mapped reads with deletion percentage = 4.7% homopolymer indels = 51.68% >>>>>>> Coverage mean coverageData = 0.2365X std coverageData = 1.0404X There is a 15.22% of reference with a coverageData >= 1X There is a 5.2% of reference with a coverageData >= 2X There is a 1.7% of reference with a coverageData >= 3X There is a 0.66% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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% 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 57706415 0.23151964383671486 0.9600931461767995 chr2 243199373 63868849 0.2626192995982765 1.6956221431293537 chr3 198022430 49022921 0.2475624655247388 0.6868080961058148 chr4 191154276 45833968 0.23977474613228114 0.958834900317845 chr5 180915260 44093960 0.24372714606827528 0.6707323601245455 chr6 171115067 43824979 0.256114086084541 0.9354729534878521 chr7 159138663 36889501 0.23180728243267948 0.7740798211524865 chr8 146364022 38323253 0.26183520018328 0.7541551430175196 chr9 141213431 31545778 0.22339077647649536 1.1278551949859073 chr10 135534747 36780030 0.27136974697713495 2.2192471486813363 chr11 135006516 34572449 0.25607985469382827 0.8479345077023548 chr12 133851895 32565541 0.2432953302603598 0.6955127635242033 chr13 115169878 22711800 0.19720260535484807 0.604551583153704 chr14 107349540 22053699 0.20543822544558646 0.6329316072442548 chr15 102531392 21571365 0.21038790734451357 0.6384668130324826 chr16 90354753 23145555 0.25616311518221957 1.4981534696163246 chr17 81195210 19050328 0.23462379123103444 0.7754081403553369 chr18 78077248 19380709 0.24822479655020627 1.2028749722427932 chr19 59128983 9895873 0.16736078481173944 0.7467832645813807 chr20 63025520 16378448 0.2598700970654427 0.7289331181576123 chr21 48129895 9395016 0.19520125693189233 0.777941338801365 chr22 51304566 8824523 0.17200268295808213 0.5995680349415939 chrMT 16571 48773 2.9432743950274576 2.8081395498063904 chrX 155270560 43209921 0.2782879188430827 0.7597878746353708 chrY 59373566 1299778 0.021891526609670035 0.7586162270573651