BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716845.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 = 2,056,013 number of mapped reads = 1,914,442 (93.11%) number of supplementary alignments = 35,699 (1.74%) number of secondary alignments = 0 number of mapped bases = 151,810,787 bp number of sequenced bases = 151,741,013 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,211 duplication rate = 3.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6121 >>>>>>> ACTG content number of A's = 38,032,109 bp (25.06%) number of C's = 28,478,427 bp (18.77%) number of T's = 47,810,726 bp (31.51%) number of G's = 37,409,490 bp (24.65%) number of N's = 10,261 bp (0.01%) GC percentage = 43.42% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 998,894 number of insertions = 13,091 mapped reads with insertion percentage = 0.67% number of deletions = 36,537 mapped reads with deletion percentage = 1.88% homopolymer indels = 43.48% >>>>>>> Coverage mean coverageData = 0.049X std coverageData = 0.4729X There is a 4.16% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 14622897 0.058667444603879244 1.0580616157868978 chr2 243199373 12923960 0.05314141989996002 0.47947442872420337 chr3 198022430 9632150 0.04864171195151983 0.2473089701358238 chr4 191154276 9998766 0.052307310143561735 0.3277223599778201 chr5 180915260 8347773 0.04614189538240168 0.2433685370343568 chr6 171115067 8584555 0.050168317439866356 0.2785450914103423 chr7 159138663 8308736 0.05221066862928213 0.5634413895448752 chr8 146364022 7735477 0.052850945842414745 0.5126977528520165 chr9 141213431 6387451 0.04523260255605573 0.3817891804753987 chr10 135534747 7262287 0.05358247357779035 0.4348329714297972 chr11 135006516 8504920 0.0629963667827707 0.4978829763599652 chr12 133851895 6549059 0.048927652462447395 0.2515785203056972 chr13 115169878 5349302 0.046447057971182364 0.2447670021359754 chr14 107349540 4577500 0.042641076990176205 0.2533253356594144 chr15 102531392 4369245 0.0426137294615097 0.23210245010522018 chr16 90354753 3504197 0.03878265264030991 0.2478377138088312 chr17 81195210 4914820 0.060530910628841285 0.33786739943648064 chr18 78077248 4085536 0.052326844306807535 0.6393453599759469 chr19 59128983 2748962 0.04649093998454193 0.7351184567015475 chr20 63025520 3197229 0.0507291173480203 0.27002589799082144 chr21 48129895 2132833 0.044314100415136996 0.2804644451362224 chr22 51304566 1780510 0.0347047083489606 0.2097701110935278 chrMT 16571 15192 0.9167823305775149 1.1675483608724802 chrX 155270560 5842593 0.03762846607882396 0.26038132235486783 chrY 59373566 434837 0.007323747406379465 0.2635380919016802