BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082979.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 = 3,555,530 number of mapped reads = 2,849,468 (80.14%) number of supplementary alignments = 18,726 (0.53%) number of secondary alignments = 0 number of mapped bases = 196,038,122 bp number of sequenced bases = 195,963,537 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,198 duplication rate = 2.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1406 >>>>>>> ACTG content number of A's = 56,739,207 bp (28.95%) number of C's = 36,202,348 bp (18.47%) number of T's = 62,700,871 bp (32%) number of G's = 40,301,298 bp (20.57%) number of N's = 19,813 bp (0.01%) GC percentage = 39.04% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,818,118 number of insertions = 16,588 mapped reads with insertion percentage = 0.58% number of deletions = 43,530 mapped reads with deletion percentage = 1.51% homopolymer indels = 48.07% >>>>>>> Coverage mean coverageData = 0.0633X std coverageData = 0.4394X There is a 5.12% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 18976049 0.07613240409940644 0.6962427213795495 chr2 243199373 20237003 0.08321157554958006 0.5358646103796401 chr3 198022430 14033825 0.07086987570044465 0.3139363999240881 chr4 191154276 11277007 0.05899427015694904 0.29794431755216877 chr5 180915260 10433453 0.057670386677165876 0.2851261265950217 chr6 171115067 15130519 0.08842306680100824 0.4929887866006374 chr7 159138663 10199141 0.06408964866067776 0.387218957667222 chr8 146364022 15989735 0.10924634880558283 0.6208055833202694 chr9 141213431 6394270 0.045280891163957344 0.3904090666680994 chr10 135534747 7386915 0.054502001615866075 0.36586992258237283 chr11 135006516 8249928 0.06110762831625104 0.37931576113670007 chr12 133851895 6255283 0.04673286844388718 0.26167526181417206 chr13 115169878 5214375 0.04527551032050238 0.25082768853541304 chr14 107349540 4167526 0.03882202010367254 0.2879330509736871 chr15 102531392 3725690 0.03633706640791534 0.22331496005939816 chr16 90354753 7504722 0.08305840867054332 0.39428066197216133 chr17 81195210 4815382 0.05930623247356587 0.33490728493179267 chr18 78077248 5368148 0.06875431879976097 0.9669298872819398 chr19 59128983 2601471 0.043996545653423466 0.5203515287574217 chr20 63025520 3523077 0.05589921352493403 0.3037851121311168 chr21 48129895 4024662 0.08362083482625507 0.3543045218470814 chr22 51304566 2309184 0.04500932723999653 0.24893610541140332 chrMT 16571 134352 8.107657956671293 6.158760754667116 chrX 155270560 7774704 0.05007197758544826 0.29817096506381363 chrY 59373566 311701 0.0052498278442632195 0.10979050567291995