BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819028.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 502,539 number of mapped reads = 456,385 (90.82%) number of supplementary alignments = 1,979 (0.39%) number of secondary alignments = 0 number of mapped bases = 26,116,298 bp number of sequenced bases = 26,109,516 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,664 duplication rate = 0.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9937 >>>>>>> ACTG content number of A's = 6,632,766 bp (25.4%) number of C's = 5,090,526 bp (19.5%) number of T's = 7,722,846 bp (29.58%) number of G's = 6,662,809 bp (25.52%) number of N's = 569 bp (0%) GC percentage = 45.02% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 128,252 number of insertions = 1,792 mapped reads with insertion percentage = 0.39% number of deletions = 4,040 mapped reads with deletion percentage = 0.88% homopolymer indels = 39.61% >>>>>>> Coverage mean coverageData = 0.0084X std coverageData = 0.1018X There is a 0.81% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 2945623 0.011817916393476107 0.1332926274262264 chr2 243199373 2160217 0.00888249411728541 0.10953869665823468 chr3 198022430 1718574 0.008678683520851653 0.09594764702670416 chr4 191154276 1664359 0.008706888670384752 0.09845891845375439 chr5 180915260 1307755 0.007228549985225127 0.08787345902541763 chr6 171115067 1357454 0.007932989325831839 0.09301465141448373 chr7 159138663 1119299 0.007033482491932209 0.0912544976134431 chr8 146364022 1641517 0.011215303990484765 0.11361012255275763 chr9 141213431 949815 0.006726095338622571 0.09506893263176791 chr10 135534747 1244657 0.009183305591738774 0.11141195671349781 chr11 135006516 825958 0.0061179121161826 0.08665810250258625 chr12 133851895 1163719 0.008694079377807837 0.09618631567430024 chr13 115169878 792516 0.006881278453729021 0.08519647142268184 chr14 107349540 917922 0.008550777208733266 0.09696499860973462 chr15 102531392 751798 0.007332368997779724 0.08807163874487405 chr16 90354753 790557 0.008749478845899784 0.09980552050000029 chr17 81195210 591761 0.007288126972022118 0.08833840917774766 chr18 78077248 652510 0.008357236156684211 0.1364208480669375 chr19 59128983 524855 0.008876442200942303 0.11210767962469162 chr20 63025520 834539 0.013241287021511287 0.11954027161982493 chr21 48129895 336891 0.006999620506132415 0.08861402674520308 chr22 51304566 312191 0.006085052936613868 0.08005726720842812 chrMT 16571 5971 0.3603282843521815 0.6196878436789537 chrX 155270560 1430438 0.009212551303994782 0.10242992133001473 chrY 59373566 75402 0.0012699590925699157 0.04225513812563348