BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234039.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 = 4,471,942 number of mapped reads = 4,132,937 (92.42%) number of supplementary alignments = 36,390 (0.81%) number of secondary alignments = 0 number of mapped bases = 261,861,016 bp number of sequenced bases = 261,746,224 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,067,549 duplication rate = 18.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 32.5938 >>>>>>> ACTG content number of A's = 63,204,073 bp (24.15%) number of C's = 49,816,844 bp (19.03%) number of T's = 83,650,520 bp (31.96%) number of G's = 65,050,066 bp (24.85%) number of N's = 24,721 bp (0.01%) GC percentage = 43.88% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 1,495,653 number of insertions = 17,280 mapped reads with insertion percentage = 0.41% number of deletions = 64,634 mapped reads with deletion percentage = 1.55% homopolymer indels = 42.93% >>>>>>> Coverage mean coverageData = 0.0846X std coverageData = 1.1134X There is a 3.9% of reference with a coverageData >= 1X There is a 1.88% of reference with a coverageData >= 2X There is a 1.03% of reference with a coverageData >= 3X There is a 0.59% of reference with a coverageData >= 4X There is a 0.35% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 19822827 0.07952969954686692 1.4704411409812925 chr2 243199373 4485369 0.018443176660656934 2.388277031227867 chr3 198022430 2088031 0.010544416609774964 0.1940159763245065 chr4 191154276 2422506 0.012673041119938118 0.2423465555928964 chr5 180915260 8292943 0.04583882531523322 0.41591959229059716 chr6 171115067 20174868 0.11790234696281889 0.9570099526232512 chr7 159138663 2268195 0.014252947443701975 0.42735990000063306 chr8 146364022 17434743 0.11911904825900453 1.007223150964148 chr9 141213431 7892516 0.05589068932118787 0.5197800865474967 chr10 135534747 6667556 0.049194440153416896 0.44854807211953435 chr11 135006516 7744048 0.05736054991597591 0.4903814837003531 chr12 133851895 5514718 0.04120014886602838 0.38588687280059697 chr13 115169878 20973844 0.18211223597892498 0.8570107173148444 chr14 107349540 2635746 0.02455293241126138 0.5871009459132257 chr15 102531392 8502041 0.08292134568893789 0.5960760456959057 chr16 90354753 28189637 0.31198842411754474 1.1752604788485648 chr17 81195210 36452917 0.4489540331258457 1.6324346614630523 chr18 78077248 1483775 0.0190039356919957 2.6591284556045123 chr19 59128983 28486376 0.4817667166709091 1.6888868986170413 chr20 63025520 5630430 0.08933571670650238 0.7867217032828302 chr21 48129895 13549500 0.28151941740159625 1.0157854511554876 chr22 51304566 8436752 0.16444446679463187 0.7442865734808022 chrMT 16571 60739 3.6653792770502687 3.7822432717659313 chrX 155270560 2046615 0.01318095973892282 0.4387076800264005 chrY 59373566 604324 0.010178334243895675 0.3416645389940189