BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716507.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 = 2,348,065 number of mapped reads = 2,078,214 (88.51%) number of supplementary alignments = 11,393 (0.49%) number of secondary alignments = 0 number of mapped bases = 119,461,575 bp number of sequenced bases = 119,428,450 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,535 duplication rate = 2.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2763 >>>>>>> ACTG content number of A's = 30,848,300 bp (25.83%) number of C's = 24,525,463 bp (20.54%) number of T's = 35,791,369 bp (29.97%) number of G's = 28,261,562 bp (23.66%) number of N's = 1,756 bp (0%) GC percentage = 44.2% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 650,042 number of insertions = 7,464 mapped reads with insertion percentage = 0.36% number of deletions = 19,462 mapped reads with deletion percentage = 0.93% homopolymer indels = 42.42% >>>>>>> Coverage mean coverageData = 0.0386X std coverageData = 0.3748X There is a 3.39% of reference with a coverageData >= 1X There is a 0.32% 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 8715751 0.03496782060173884 0.6513871142553388 chr2 243199373 9435320 0.03879664607523474 0.4522029045805444 chr3 198022430 6823716 0.0344593084732876 0.20392604135978257 chr4 191154276 7718691 0.040379379219327535 0.25506933882233923 chr5 180915260 6197340 0.03425548513707467 0.2093579089694983 chr6 171115067 5204227 0.03041361050923704 0.22719259318273774 chr7 159138663 7690285 0.048324428866164344 0.5273595446964058 chr8 146364022 5242948 0.03582128946962116 0.32398487900361683 chr9 141213431 4868900 0.03447901495998635 0.3963916927993543 chr10 135534747 4706054 0.03472212184820768 0.3624004566301639 chr11 135006516 4485620 0.03322521114462357 0.31189679285272554 chr12 133851895 9137497 0.06826572757897824 0.3320758214368735 chr13 115169878 4644318 0.04032580463443749 0.21998783742018038 chr14 107349540 4456548 0.04151436512909138 0.26679712071294276 chr15 102531392 3220584 0.03141071175547875 0.19692192336698675 chr16 90354753 3605640 0.0399053716631819 0.2539502190973179 chr17 81195210 3941335 0.04854147184298187 0.2560323640011467 chr18 78077248 3768018 0.04826012822583091 0.7720701808011151 chr19 59128983 2183467 0.03692718679095157 0.512402662623094 chr20 63025520 3726967 0.05913425228383677 0.281087766252336 chr21 48129895 1442992 0.029981199834323347 0.22926321106524053 chr22 51304566 1372792 0.026757696381253863 0.17776629515924958 chrMT 16571 4368 0.26359302395751616 0.5330558629030285 chrX 155270560 6514332 0.041954714403039446 0.2942917082811987 chrY 59373566 353865 0.005959975521766706 0.13317171781928697