BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237821.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 = 2,149,294 number of mapped reads = 266,682 (12.41%) number of supplementary alignments = 2,748 (0.13%) number of secondary alignments = 0 number of mapped bases = 15,280,940 bp number of sequenced bases = 15,270,863 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,912 duplication rate = 8.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.1245 >>>>>>> ACTG content number of A's = 4,264,540 bp (27.93%) number of C's = 2,756,041 bp (18.05%) number of T's = 4,882,292 bp (31.97%) number of G's = 3,347,234 bp (21.92%) number of N's = 20,756 bp (0.14%) GC percentage = 39.97% >>>>>>> Mismatches and indels general error rate = 0.0151 number of mismatches = 225,242 number of insertions = 3,410 mapped reads with insertion percentage = 1.25% number of deletions = 5,870 mapped reads with deletion percentage = 2.14% homopolymer indels = 38.8% >>>>>>> Coverage mean coverageData = 0.0049X std coverageData = 0.1382X There is a 0.35% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 1102736 0.004424205627154686 0.14083187548766607 chr2 243199373 1353165 0.005564015167095024 0.18565221337720916 chr3 198022430 898265 0.0045361780481130345 0.1248666623427193 chr4 191154276 974982 0.005100497987290642 0.12845829826140334 chr5 180915260 924972 0.005112736205889984 0.14397315013362005 chr6 171115067 828538 0.0048419932535806445 0.119163010272919 chr7 159138663 982828 0.0061759221893173755 0.17363492756225635 chr8 146364022 697306 0.004764189931867273 0.10474883280237156 chr9 141213431 668477 0.0047338060924247355 0.10845147503053743 chr10 135534747 798178 0.005889102371659719 0.11830533869526477 chr11 135006516 656842 0.004865261466342854 0.11957206730976588 chr12 133851895 621424 0.004642623849292533 0.13155585097291694 chr13 115169878 405101 0.0035174214563290585 0.08929206791825153 chr14 107349540 462815 0.0043112900157746365 0.10541656626583702 chr15 102531392 412236 0.004020583276583234 0.13481075402291912 chr16 90354753 581426 0.006434924347588002 0.11621281930656414 chr17 81195210 325289 0.004006258497268497 0.12138973719343091 chr18 78077248 441451 0.005654028687076675 0.1510576579374154 chr19 59128983 236449 0.003998868033972443 0.09319472786771738 chr20 63025520 408093 0.006475043760051484 0.19579340938250933 chr21 48129895 290103 0.0060275012027348075 0.12711145114917183 chr22 51304566 205801 0.0040113583652573925 0.16689736019357962 chrMT 16571 5358 0.32333594834349166 0.7226812434392847 chrX 155270560 952807 0.006136430499123594 0.19316487932334636 chrY 59373566 46298 7.797746222620349E-4 0.034540392282184494