BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236120.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,508,939 number of mapped reads = 3,045,881 (86.8%) number of supplementary alignments = 24,627 (0.7%) number of secondary alignments = 0 number of mapped bases = 203,215,095 bp number of sequenced bases = 203,102,979 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 249,285 duplication rate = 6.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6565 >>>>>>> ACTG content number of A's = 57,370,861 bp (28.25%) number of C's = 35,407,194 bp (17.43%) number of T's = 66,833,633 bp (32.91%) number of G's = 43,377,974 bp (21.36%) number of N's = 113,317 bp (0.06%) GC percentage = 38.79% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,686,036 number of insertions = 14,805 mapped reads with insertion percentage = 0.48% number of deletions = 64,418 mapped reads with deletion percentage = 2.09% homopolymer indels = 46.21% >>>>>>> Coverage mean coverageData = 0.0656X std coverageData = 0.7668X There is a 4.45% of reference with a coverageData >= 1X There is a 1.33% of reference with a coverageData >= 2X There is a 0.43% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 20337070 0.08159285589101903 1.0035638947710468 chr2 243199373 19216834 0.07901679088621663 0.6688668031358712 chr3 198022430 16722223 0.08444610542351187 0.39718557683852407 chr4 191154276 10916411 0.05710785669267477 0.34565592805761375 chr5 180915260 6546146 0.036183492757880124 0.26076191838970136 chr6 171115067 25661641 0.14996716215527647 0.9649821213200621 chr7 159138663 9768066 0.06138084746885174 0.61256260938678 chr8 146364022 16570879 0.11321688741239976 2.476720866166639 chr9 141213431 5615508 0.039766104117957446 0.45989383661325706 chr10 135534747 5978118 0.04410764126781452 0.5087966636237329 chr11 135006516 4438611 0.032877013136165964 0.3125825697403568 chr12 133851895 7668630 0.05729190460844802 0.3375194299119577 chr13 115169878 11419210 0.0991510123853739 0.4384248765716383 chr14 107349540 3610945 0.033637265702302965 0.2743307942644536 chr15 102531392 6294040 0.06138646786342274 0.33994062073784614 chr16 90354753 2966857 0.03283564949815092 0.28866754195585625 chr17 81195210 3420996 0.04213297804143865 0.30078677227683237 chr18 78077248 5559807 0.07120905439699923 0.8771505219203016 chr19 59128983 2051284 0.03469168411031186 0.5940074639912956 chr20 63025520 3315952 0.05261284635176354 0.32692940763851797 chr21 48129895 3706083 0.07700168471175763 0.3951798161776799 chr22 51304566 837797 0.016329872081950757 0.1651312190386903 chrMT 16571 138572 8.362319715165047 5.817748510704082 chrX 155270560 9990646 0.0643434660118441 0.3873198808354011 chrY 59373566 462769 0.007794192452580665 0.18359511820515784