BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080904.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 = 4,775,560 number of mapped reads = 4,306,643 (90.18%) number of supplementary alignments = 58,740 (1.23%) number of secondary alignments = 0 number of mapped bases = 298,451,654 bp number of sequenced bases = 298,343,944 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 274,029 duplication rate = 5.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0129 >>>>>>> ACTG content number of A's = 86,953,543 bp (29.15%) number of C's = 53,255,416 bp (17.85%) number of T's = 94,878,487 bp (31.8%) number of G's = 61,774,387 bp (20.71%) number of N's = 1,482,111 bp (0.5%) GC percentage = 38.56% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 3,316,114 number of insertions = 21,877 mapped reads with insertion percentage = 0.5% number of deletions = 65,604 mapped reads with deletion percentage = 1.51% homopolymer indels = 49.98% >>>>>>> Coverage mean coverageData = 0.0964X std coverageData = 0.5883X There is a 5.96% of reference with a coverageData >= 1X There is a 2.15% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 24036245 0.096434042585595 0.7348666399282064 chr2 243199373 25746293 0.10586496454495382 0.5679615520148638 chr3 198022430 21688598 0.1095259663261379 0.4920945322776546 chr4 191154276 22675220 0.11862261454198388 0.51931475548312 chr5 180915260 18969468 0.10485278024639823 0.48417193695097716 chr6 171115067 17437933 0.1019076420663763 0.5255025969608528 chr7 159138663 16378886 0.1029221038510296 0.659309945750461 chr8 146364022 15561826 0.10632275464526385 1.197839491925528 chr9 141213431 13177819 0.09331845354001773 0.5432062953233098 chr10 135534747 12705884 0.09374632174581769 0.506986274067653 chr11 135006516 14347308 0.10627122619770442 0.5920531783792183 chr12 133851895 14238250 0.10637316714866084 0.4868964556583845 chr13 115169878 9498710 0.0824756452377244 0.427376200625998 chr14 107349540 8377146 0.07803616112374585 0.4280595101705664 chr15 102531392 7750255 0.07558909372848464 0.4073714155202377 chr16 90354753 7449772 0.08245025029286505 0.43824352817542706 chr17 81195210 5815564 0.07162447144357408 0.4261984480124622 chr18 78077248 8214602 0.10521121338702921 0.8257812789399438 chr19 59128983 3927130 0.06641632919680016 0.5459960110785828 chr20 63025520 5081224 0.08062169102293801 0.4267438875773606 chr21 48129895 3833008 0.07963881907492215 0.4411360854231301 chr22 51304566 2399700 0.04677361465254379 0.3127784199064793 chrMT 16571 24745 1.4932713777080442 1.805588776264168 chrX 155270560 18508645 0.1192025391033561 0.5375145626795075 chrY 59373566 607423 0.010230529188696533 0.1753680583896567