BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716839.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 = 2,607,929 number of mapped reads = 2,359,210 (90.46%) number of supplementary alignments = 14,217 (0.55%) number of secondary alignments = 0 number of mapped bases = 136,220,651 bp number of sequenced bases = 136,184,246 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 125,304 duplication rate = 4.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5143 >>>>>>> ACTG content number of A's = 34,269,632 bp (25.16%) number of C's = 25,221,928 bp (18.52%) number of T's = 43,807,330 bp (32.17%) number of G's = 32,884,368 bp (24.15%) number of N's = 988 bp (0%) GC percentage = 42.67% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 677,230 number of insertions = 9,565 mapped reads with insertion percentage = 0.4% number of deletions = 23,340 mapped reads with deletion percentage = 0.98% homopolymer indels = 42.21% >>>>>>> Coverage mean coverageData = 0.044X std coverageData = 0.3588X There is a 3.72% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.09% 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 16123532 0.06468803140915745 0.5754894361990714 chr2 243199373 13779273 0.05665834097360111 0.5339471064083208 chr3 198022430 8541067 0.04313181592610494 0.24035101974383727 chr4 191154276 5789718 0.030288195070247867 0.23152747894317519 chr5 180915260 9802869 0.05418486533419016 0.2696401869275072 chr6 171115067 5192830 0.03034700620489486 0.2302798035137929 chr7 159138663 9056533 0.056909696419907715 0.5682532759189955 chr8 146364022 6118180 0.041801119676801446 0.31698170405722403 chr9 141213431 3745715 0.026525203541014453 0.2696378536108525 chr10 135534747 6065121 0.0447495652166599 0.3116831314402088 chr11 135006516 5917818 0.04383357318842299 0.34836437245354934 chr12 133851895 5380122 0.04019458969930908 0.23406523041697888 chr13 115169878 3962308 0.03440403053999936 0.21349009166280172 chr14 107349540 3001383 0.027958974020755003 0.20484889347579988 chr15 102531392 5791723 0.05648731463628232 0.2774820866228146 chr16 90354753 4038335 0.04469421769101621 0.261792440122319 chr17 81195210 5083287 0.06260574977267748 0.31988769374147824 chr18 78077248 4326217 0.0554094452714317 0.5900391169033459 chr19 59128983 2116012 0.03578637569328733 0.40664170202930094 chr20 63025520 3618938 0.05742020057906702 0.28266986489981644 chr21 48129895 1744652 0.03624882206786447 0.23361962640671002 chr22 51304566 1578160 0.030760614951893365 0.2010141777415147 chrMT 16571 25927 1.5646008086416028 1.5471972951470978 chrX 155270560 5107632 0.03289504462404206 0.24102506880282537 chrY 59373566 313299 0.005276742178497414 0.1357633937258961