BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006045.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 6,485,278 number of mapped reads = 5,674,059 (87.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,881,663 number of mapped paired reads (second in pair) = 2,792,396 number of mapped paired reads (both in pair) = 5,248,804 number of mapped paired reads (singletons) = 425,255 number of mapped bases = 219,531,611 bp number of sequenced bases = 219,507,624 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 168,242 duplication rate = 2.48% >>>>>>> Insert size mean insert size = 50,319.8134 std insert size = 2,190,680.6874 median insert size = 105 >>>>>>> Mapping quality mean mapping quality = 47.5994 >>>>>>> ACTG content number of A's = 60,206,792 bp (27.43%) number of C's = 48,172,572 bp (21.95%) number of T's = 61,495,999 bp (28.02%) number of G's = 49,542,809 bp (22.57%) number of N's = 89,452 bp (0.04%) GC percentage = 44.52% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,201,431 number of insertions = 6,537 mapped reads with insertion percentage = 0.12% number of deletions = 18,536 mapped reads with deletion percentage = 0.33% homopolymer indels = 45.46% >>>>>>> Coverage mean coverageData = 0.0709X std coverageData = 0.3825X There is a 5.54% of reference with a coverageData >= 1X There is a 1.16% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 18585247 0.07456449627060308 0.42882105719963654 chr2 243199373 19062830 0.07838354912206126 0.4405524769985078 chr3 198022430 15126688 0.0763887606065636 0.3354093741577113 chr4 191154276 13911844 0.07277809469457015 0.35127526249747054 chr5 180915260 13380768 0.07396152209603546 0.3312608670898104 chr6 171115067 12683012 0.07411978513849982 0.3509133405736856 chr7 159138663 12051166 0.07572745537016357 0.5126105173038772 chr8 146364022 11138418 0.07610079203754049 0.40724749620572964 chr9 141213431 9444219 0.06687904212170867 0.3702724697195305 chr10 135534747 10597316 0.07818892375989753 0.3802528623881245 chr11 135006516 10243066 0.0758709009274782 0.47485735129276946 chr12 133851895 10134347 0.07571313801720925 0.33799174770060947 chr13 115169878 6908124 0.059982038011709975 0.2978220639155713 chr14 107349540 6776643 0.06312689369698277 0.3214509280308844 chr15 102531392 6623221 0.0645970065441031 0.3105433576954613 chr16 90354753 6835491 0.0756517036796061 0.38759014647432366 chr17 81195210 6350053 0.07820723660915466 0.37530449713287956 chr18 78077248 5769146 0.07389023240163382 0.5029345542667835 chr19 59128983 4755554 0.08042678494910017 0.4408454708710141 chr20 63025520 5049797 0.08012305174158024 0.35550451512938264 chr21 48129895 2936133 0.06100435083018569 0.345133491642716 chr22 51304566 2916221 0.056841354042445266 0.3151448378282367 chrMT 16571 45786 2.7630197332689637 3.740104160380814 chrX 155270560 6672845 0.042975596919338735 0.2710375572147033 chrY 59373566 1533676 0.0258309564899639 0.25661192619838696