BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231774.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 = 725,311 number of mapped reads = 495,255 (68.28%) number of supplementary alignments = 3,106 (0.43%) number of secondary alignments = 0 number of mapped bases = 32,256,248 bp number of sequenced bases = 32,235,619 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,507 duplication rate = 2.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9528 >>>>>>> ACTG content number of A's = 8,979,985 bp (27.86%) number of C's = 5,521,814 bp (17.13%) number of T's = 10,652,304 bp (33.05%) number of G's = 7,080,121 bp (21.96%) number of N's = 1,395 bp (0%) GC percentage = 39.09% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 288,964 number of insertions = 2,751 mapped reads with insertion percentage = 0.55% number of deletions = 11,894 mapped reads with deletion percentage = 2.36% homopolymer indels = 45.2% >>>>>>> Coverage mean coverageData = 0.0104X std coverageData = 0.1305X There is a 0.95% 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 3299987 0.013239634014793488 0.20632216624247232 chr2 243199373 2428541 0.009985802882805952 0.1264885142429292 chr3 198022430 1282549 0.006476786493328054 0.08687575382726848 chr4 191154276 867698 0.00453925498375982 0.073245979464079 chr5 180915260 1491872 0.008246247442034465 0.09830833576940384 chr6 171115067 2978327 0.017405404750243297 0.15324528717556707 chr7 159138663 1899720 0.011937513890009244 0.12747798050455916 chr8 146364022 2478154 0.016931442345851908 0.21419617793657084 chr9 141213431 1473177 0.010432272550618786 0.11828817491443937 chr10 135534747 1348356 0.00994841566347558 0.11355606963592557 chr11 135006516 1283744 0.00950875585886536 0.11184129581737301 chr12 133851895 1516421 0.011329096237300188 0.11589809700371233 chr13 115169878 1072907 0.00931586469163404 0.10484991381481379 chr14 107349540 1205071 0.011225674558083808 0.11585562614672461 chr15 102531392 604731 0.005898008289987909 0.08477848554789193 chr16 90354753 1309563 0.01449357069240176 0.13072286729808388 chr17 81195210 852669 0.010501469236916808 0.11106690008532419 chr18 78077248 686924 0.008798004765741744 0.16450091307489825 chr19 59128983 892861 0.015100225890913766 0.14874405981300876 chr20 63025520 1254605 0.019906301447413684 0.15296536969599606 chr21 48129895 570279 0.011848748059807734 0.11807096437683064 chr22 51304566 117091 0.002282272497929327 0.05092751239397819 chrMT 16571 33819 2.0408545048578843 1.8750709640668575 chrX 155270560 1245061 0.00801865466318921 0.09821346757481648 chrY 59373566 62121 0.0010462736902142613 0.03595599861098593