BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238243.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 = 819,029 number of mapped reads = 308,754 (37.7%) number of supplementary alignments = 2,833 (0.35%) number of secondary alignments = 0 number of mapped bases = 18,340,731 bp number of sequenced bases = 18,333,105 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,287 duplication rate = 8.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0972 >>>>>>> ACTG content number of A's = 5,177,958 bp (28.24%) number of C's = 3,776,994 bp (20.6%) number of T's = 5,367,586 bp (29.28%) number of G's = 4,008,112 bp (21.86%) number of N's = 2,455 bp (0.01%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 182,702 number of insertions = 1,604 mapped reads with insertion percentage = 0.51% number of deletions = 4,739 mapped reads with deletion percentage = 1.52% homopolymer indels = 44.14% >>>>>>> Coverage mean coverageData = 0.0059X std coverageData = 0.2644X There is a 0.37% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 1464434 0.005875347447980882 0.2747415164138617 chr2 243199373 1514517 0.006227470824935063 0.37637614969364974 chr3 198022430 1194336 0.006031316755379681 0.1637726151794651 chr4 191154276 1162232 0.00608007324931617 0.20693978978159613 chr5 180915260 1113091 0.006152554516407295 0.17906154112561823 chr6 171115067 1043144 0.006096155167913998 0.2581861673390511 chr7 159138663 969291 0.0060908580085280726 0.1771151720162894 chr8 146364022 985670 0.006734373560737488 0.18916809882835034 chr9 141213431 700527 0.004960767506597867 0.1401327736870956 chr10 135534747 932910 0.006883179558375536 0.16525028497257988 chr11 135006516 758260 0.005616469652472181 0.126924242752521 chr12 133851895 842942 0.006297572402691796 0.16195074082374017 chr13 115169878 572170 0.004968052497198964 0.22925901279958266 chr14 107349540 633769 0.005903788688801088 0.5884947499723585 chr15 102531392 542537 0.005291423333060766 0.6672881154122682 chr16 90354753 554654 0.006138625601688048 0.1409805801392166 chr17 81195210 440716 0.005427857135907401 0.15257967726756552 chr18 78077248 478864 0.006133207973723664 0.14283795014570472 chr19 59128983 394128 0.006665563654291162 0.13418484730250993 chr20 63025520 372840 0.005915698910536557 0.13476286553103276 chr21 48129895 243829 0.005066061332566796 0.11091531279516105 chr22 51304566 202084 0.003938908673352777 0.10373787637009406 chrMT 16571 9130 0.5509625248928851 1.2420943569760081 chrX 155270560 1153284 0.007427576740883784 0.2801723497069474 chrY 59373566 61372 0.001033658648698985 0.06722494429771815