BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524395.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 = 2,179,436 number of mapped reads = 2,021,687 (92.76%) number of supplementary alignments = 8,104 (0.37%) number of secondary alignments = 0 number of mapped bases = 118,782,984 bp number of sequenced bases = 118,748,481 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,287 duplication rate = 3.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.987 >>>>>>> ACTG content number of A's = 30,618,802 bp (25.78%) number of C's = 22,203,890 bp (18.7%) number of T's = 37,973,114 bp (31.98%) number of G's = 27,936,458 bp (23.53%) number of N's = 16,217 bp (0.01%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 574,079 number of insertions = 8,999 mapped reads with insertion percentage = 0.44% number of deletions = 21,631 mapped reads with deletion percentage = 1.06% homopolymer indels = 42.98% >>>>>>> Coverage mean coverageData = 0.0384X std coverageData = 0.3751X There is a 3.35% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 9783447 0.03925144483391277 0.8126202833957861 chr2 243199373 9598717 0.03946851047185882 0.3965972532494853 chr3 198022430 8299914 0.04191400943822374 0.22661484381734734 chr4 191154276 7987178 0.041783935819463436 0.2577471947943797 chr5 180915260 7228417 0.03995471139361047 0.22394646787367872 chr6 171115067 4568644 0.026699250277008042 0.20114096594958233 chr7 159138663 6838864 0.04297424567403837 0.5631462457427634 chr8 146364022 6354013 0.04341239679789614 0.339811186017173 chr9 141213431 4372094 0.03096089351444198 0.264716076834385 chr10 135534747 6034054 0.04452034724350059 0.32999646060055665 chr11 135006516 4921820 0.03645616630829878 0.28770471458427976 chr12 133851895 5541084 0.04139712777320037 0.24073522102241496 chr13 115169878 3887086 0.03375089100988715 0.20643452433831314 chr14 107349540 3316566 0.030895018273948822 0.2022783566835416 chr15 102531392 3611274 0.03522115451236632 0.2094713189973538 chr16 90354753 3608923 0.039941706221033 0.23495882474026603 chr17 81195210 3202139 0.039437535785670115 0.25273785064087945 chr18 78077248 3295758 0.04221150315134058 0.495407155941739 chr19 59128983 3278244 0.05544225240606624 0.5620837425676436 chr20 63025520 3262490 0.05176458678960523 0.2634854049621871 chr21 48129895 1647641 0.03423321409697653 0.23594234706470582 chr22 51304566 804519 0.01568123585725294 0.13739226098499854 chrMT 16571 13191 0.796029207651922 1.017218804893399 chrX 155270560 6965505 0.04486043587399955 0.2670483077697113 chrY 59373566 361402 0.006086917534985182 0.17418032737352065