BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084282.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,729,219 number of mapped reads = 2,442,813 (89.51%) number of supplementary alignments = 17,230 (0.63%) number of secondary alignments = 0 number of mapped bases = 160,193,442 bp number of sequenced bases = 160,137,820 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,998 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7944 >>>>>>> ACTG content number of A's = 43,875,201 bp (27.4%) number of C's = 30,706,918 bp (19.18%) number of T's = 49,083,793 bp (30.65%) number of G's = 36,268,043 bp (22.65%) number of N's = 203,865 bp (0.13%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 1,670,175 number of insertions = 12,413 mapped reads with insertion percentage = 0.5% number of deletions = 34,514 mapped reads with deletion percentage = 1.4% homopolymer indels = 46.03% >>>>>>> Coverage mean coverageData = 0.0517X std coverageData = 0.3603X There is a 4.41% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.1% 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 0.01% 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 16214701 0.06505380381780473 0.5869618457652717 chr2 243199373 14475848 0.059522554772375995 0.43257129444507897 chr3 198022430 11054577 0.05582487297019838 0.27544687438303206 chr4 191154276 7427201 0.03885448526403877 0.23389381531350842 chr5 180915260 8224191 0.04545880209331153 0.24094208439573558 chr6 171115067 7555050 0.0441518688707874 0.2707377035112638 chr7 159138663 9035274 0.05677610851864452 0.5084122345224023 chr8 146364022 7673692 0.052428813414269256 0.3376678398474551 chr9 141213431 5540667 0.039236119119575814 0.28178473111254193 chr10 135534747 11258162 0.08306476567223016 0.5349593835270524 chr11 135006516 9135207 0.06766493403918371 0.3903420066503654 chr12 133851895 8585546 0.06414213261605299 0.28829290190135 chr13 115169878 3866148 0.03356909000111991 0.20756031060361446 chr14 107349540 4551231 0.04239637170312979 0.23807339741539105 chr15 102531392 3230574 0.03150814532977374 0.2093789038426803 chr16 90354753 3139902 0.03475082268223344 0.23699719688623191 chr17 81195210 4573084 0.056322090921373316 0.2947591049161507 chr18 78077248 4030040 0.051616061057889746 0.470451052743825 chr19 59128983 3820373 0.06461083560324385 0.4370180041547666 chr20 63025520 3467213 0.055012842416849554 0.27088378783182937 chr21 48129895 1715684 0.035646950819236155 0.22504955947313152 chr22 51304566 1498307 0.029204164791102608 0.19176336460322654 chrMT 16571 37463 2.260756743708889 1.9268168354480244 chrX 155270560 9726898 0.06264483106134222 0.31674236931654076 chrY 59373566 356409 0.006002822872387351 0.1155571369383247