BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716750.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 853,463 number of mapped reads = 535,409 (62.73%) number of supplementary alignments = 551 (0.06%) number of secondary alignments = 0 number of mapped bases = 28,556,779 bp number of sequenced bases = 28,549,747 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,922 duplication rate = 5.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4324 >>>>>>> ACTG content number of A's = 5,779,770 bp (20.24%) number of C's = 5,104,523 bp (17.88%) number of T's = 9,421,785 bp (33%) number of G's = 8,243,245 bp (28.87%) number of N's = 424 bp (0%) GC percentage = 46.75% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 180,949 number of insertions = 1,640 mapped reads with insertion percentage = 0.31% number of deletions = 4,127 mapped reads with deletion percentage = 0.76% homopolymer indels = 42.01% >>>>>>> Coverage mean coverageData = 0.0092X std coverageData = 0.1133X There is a 0.83% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 2797775 0.011224746356800451 0.1273369203410231 chr2 243199373 2453658 0.010089080287225905 0.14410340583181808 chr3 198022430 1995882 0.010079070335618041 0.11001460470278954 chr4 191154276 1802766 0.00943094780678618 0.11058624874354898 chr5 180915260 1735105 0.009590705615435647 0.10823008274127521 chr6 171115067 1218715 0.007122195732769693 0.10019489576711611 chr7 159138663 1674521 0.010522402089051107 0.12399544106942537 chr8 146364022 1719955 0.011751214379719628 0.12202683095726162 chr9 141213431 1266523 0.008968856510539708 0.10839066790910745 chr10 135534747 1459013 0.010764863123992847 0.12444128374660665 chr11 135006516 1197793 0.008872112513443425 0.10978998373306197 chr12 133851895 1385277 0.010349326768963562 0.1130813288792229 chr13 115169878 504547 0.004380893761127367 0.07315116439050155 chr14 107349540 928345 0.008647871243789214 0.10290024497212355 chr15 102531392 571459 0.005573502796099755 0.08235889861529695 chr16 90354753 752409 0.008327276374713791 0.10550714760157558 chr17 81195210 1134429 0.013971624680815531 0.13329895662768595 chr18 78077248 760301 0.00973780479557886 0.11844809880567683 chr19 59128983 752483 0.01272612789568865 0.13918325769027062 chr20 63025520 747187 0.011855308770161674 0.12442427241813693 chr21 48129895 401767 0.008347556129096064 0.10511632914040453 chr22 51304566 319140 0.006220498970793359 0.0891250097597104 chrMT 16571 7754 0.46792589463520606 0.7241492717825669 chrX 155270560 889132 0.005726339880528543 0.08442895282578207 chrY 59373566 80843 0.0013615992005600608 0.051621755137993545