BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716753.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 = 1,575,238 number of mapped reads = 1,190,470 (75.57%) number of supplementary alignments = 2,939 (0.19%) number of secondary alignments = 0 number of mapped bases = 62,613,052 bp number of sequenced bases = 62,596,036 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,700 duplication rate = 4.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.2552 >>>>>>> ACTG content number of A's = 15,794,425 bp (25.23%) number of C's = 13,696,919 bp (21.88%) number of T's = 17,455,234 bp (27.89%) number of G's = 15,647,749 bp (25%) number of N's = 1,709 bp (0%) GC percentage = 46.88% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 328,679 number of insertions = 4,684 mapped reads with insertion percentage = 0.39% number of deletions = 10,384 mapped reads with deletion percentage = 0.87% homopolymer indels = 32.83% >>>>>>> Coverage mean coverageData = 0.0202X std coverageData = 0.1938X There is a 1.65% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.06% 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% 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 5792320 0.023238939091750548 0.22757586240102404 chr2 243199373 5282054 0.021719028033842833 0.22220414339941943 chr3 198022430 4769890 0.024087624821087186 0.19271601954862577 chr4 191154276 3539838 0.01851822556143081 0.18448431239952115 chr5 180915260 3900226 0.021558303041987723 0.17913216105048876 chr6 171115067 2780895 0.01625160804805108 0.1584089205264162 chr7 159138663 3421826 0.021502166321455143 0.21296240550445247 chr8 146364022 3596411 0.024571687432858327 0.19825419127912522 chr9 141213431 3025126 0.0214223673950674 0.18545486462410288 chr10 135534747 3286191 0.02424611454064986 0.250415322101313 chr11 135006516 2998120 0.022207224427597257 0.21298281056202628 chr12 133851895 2833126 0.02116612544036078 0.1813364871228874 chr13 115169878 1094945 0.009507216808895118 0.11789716827396467 chr14 107349540 1780805 0.01658884611894937 0.15561028677896213 chr15 102531392 1166231 0.011374379858219423 0.1299581720334894 chr16 90354753 1915190 0.021196339278355396 0.18932974020371796 chr17 81195210 2341132 0.028833375761944578 0.22039164320408194 chr18 78077248 1570443 0.020113964570062714 0.20429332793888438 chr19 59128983 1550935 0.02622969179091073 0.2254359251449046 chr20 63025520 1988327 0.03154796660146557 0.23359085881672667 chr21 48129895 751854 0.015621351345146296 0.19318452738984968 chr22 51304566 611244 0.011914027301195765 0.1330312723099464 chrMT 16571 51089 3.0830366302576793 3.006367210039535 chrX 155270560 2364688 0.015229467839878982 0.1557292633585416 chrY 59373566 200146 0.0033709614140407197 0.11864549010046349