BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240041.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 = 1,798,191 number of mapped reads = 1,523,529 (84.73%) number of supplementary alignments = 14,421 (0.8%) number of secondary alignments = 0 number of mapped bases = 97,865,436 bp number of sequenced bases = 97,830,089 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 173,322 duplication rate = 9.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1231 >>>>>>> ACTG content number of A's = 27,379,053 bp (27.99%) number of C's = 17,641,337 bp (18.03%) number of T's = 31,420,469 bp (32.12%) number of G's = 21,321,386 bp (21.79%) number of N's = 67,844 bp (0.07%) GC percentage = 39.83% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 829,342 number of insertions = 6,813 mapped reads with insertion percentage = 0.44% number of deletions = 20,598 mapped reads with deletion percentage = 1.34% homopolymer indels = 47.57% >>>>>>> Coverage mean coverageData = 0.0316X std coverageData = 0.3744X There is a 1.95% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% 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% 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 7352438 0.029498173246276484 0.7003760853315758 chr2 243199373 9016899 0.037076160554081694 0.38480916787929353 chr3 198022430 6574954 0.033203077045362996 0.2723781644975333 chr4 191154276 6993494 0.03658560062763126 0.2899969347792284 chr5 180915260 5947307 0.03287344030569892 0.27079284502887535 chr6 171115067 5866730 0.034285291779712186 0.31243134757216934 chr7 159138663 5213364 0.032759883121551675 0.39498360238903113 chr8 146364022 5355022 0.03658701043347934 0.5793076329449677 chr9 141213431 4040123 0.028610047722726885 0.3049995183370053 chr10 135534747 4250842 0.03136348496670009 0.332579362587889 chr11 135006516 4515459 0.03344623010640464 0.3100390778641023 chr12 133851895 4402490 0.03289075586117029 0.2715646520755973 chr13 115169878 3177428 0.02758905414486937 0.24942811290806896 chr14 107349540 3175546 0.02958136569565179 0.2627154907293418 chr15 102531392 2616081 0.02551492717469397 0.24056461052203146 chr16 90354753 2722666 0.030133068926656244 0.26401135695989786 chr17 81195210 2308924 0.02843670211580215 0.26482979549905206 chr18 78077248 2544991 0.032595808192419896 0.5089032050365604 chr19 59128983 1604211 0.02713070508924532 0.46908537632713854 chr20 63025520 1826110 0.028974136191180968 0.259374430230867 chr21 48129895 1306829 0.0271521265525304 0.2502885907982076 chr22 51304566 965237 0.018813861518680423 0.19728563400383212 chrMT 16571 32619 1.9684388389354897 2.2551861564353253 chrX 155270560 5816001 0.03745720373520904 0.3020943841580457 chrY 59373566 239671 0.0040366617022801025 0.10010313435719992