BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004062.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 = 2,306,937 number of mapped reads = 998,761 (43.29%) number of supplementary alignments = 11,636 (0.5%) number of secondary alignments = 0 number of mapped bases = 61,896,503 bp number of sequenced bases = 61,860,933 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 168,548 duplication rate = 12.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5859 >>>>>>> ACTG content number of A's = 17,162,031 bp (27.74%) number of C's = 11,020,532 bp (17.82%) number of T's = 20,033,725 bp (32.39%) number of G's = 13,605,736 bp (21.99%) number of N's = 38,909 bp (0.06%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 585,376 number of insertions = 4,482 mapped reads with insertion percentage = 0.44% number of deletions = 21,161 mapped reads with deletion percentage = 2.09% homopolymer indels = 44.64% >>>>>>> Coverage mean coverageData = 0.02X std coverageData = 0.2965X There is a 1.01% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 5672496 0.022758202074850596 0.3875540403343417 chr2 243199373 6468462 0.02659736297922117 0.35271463706562084 chr3 198022430 5146731 0.025990646615133447 0.29100877626870797 chr4 191154276 3386112 0.01771402696741139 0.25025423942026964 chr5 180915260 3927529 0.021709219001205315 0.2671889637286966 chr6 171115067 3344570 0.019545736437107553 0.2681287422177307 chr7 159138663 2648315 0.01664155617544682 0.25057780391678 chr8 146364022 2857994 0.019526615632358066 0.31321727784751796 chr9 141213431 2117907 0.014997914752173963 0.2356978107326163 chr10 135534747 3720380 0.027449639906731813 0.313950725868175 chr11 135006516 3398422 0.025172281314184863 0.30159420129735814 chr12 133851895 2848819 0.02128336696316477 0.2601709872719528 chr13 115169878 1384547 0.012021780556197167 0.1904251832256078 chr14 107349540 1705016 0.01588284402522824 0.25605260573567273 chr15 102531392 1224370 0.01194141595190671 0.25124289672837763 chr16 90354753 1464858 0.016212295992884845 0.2321212123831953 chr17 81195210 1427386 0.01757968234825675 0.2407145908403822 chr18 78077248 1594091 0.020416844097783774 0.32664575601779305 chr19 59128983 992085 0.016778320033003103 0.2657931895366386 chr20 63025520 893323 0.014173988568440214 0.20934892103690994 chr21 48129895 713986 0.014834563840207838 0.22025371076130568 chr22 51304566 595834 0.01161366417172304 0.1854301056704976 chrMT 16571 462972 27.93868806951904 24.643515497570675 chrX 155270560 3717611 0.02394279379168852 0.29237606118626397 chrY 59373566 182687 0.003076907996396915 0.1034684409505264