BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081777.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 = 2,800,101 number of mapped reads = 2,555,771 (91.27%) number of supplementary alignments = 20,509 (0.73%) number of secondary alignments = 0 number of mapped bases = 171,741,385 bp number of sequenced bases = 171,671,229 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 108,275 duplication rate = 2.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5022 >>>>>>> ACTG content number of A's = 47,303,206 bp (27.55%) number of C's = 33,305,113 bp (19.4%) number of T's = 51,925,889 bp (30.25%) number of G's = 39,134,936 bp (22.8%) number of N's = 2,085 bp (0%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,473,990 number of insertions = 13,459 mapped reads with insertion percentage = 0.52% number of deletions = 39,266 mapped reads with deletion percentage = 1.52% homopolymer indels = 45.1% >>>>>>> Coverage mean coverageData = 0.0555X std coverageData = 0.5608X There is a 4.75% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 13740924 0.05512894589739056 1.097404253737793 chr2 243199373 14645658 0.06022078848040451 0.7058575298006171 chr3 198022430 11411487 0.05762724455002395 0.27938971757066333 chr4 191154276 11221939 0.058706188712200194 0.32913711356587155 chr5 180915260 10378568 0.05736701260026379 0.27232046574115043 chr6 171115067 9867469 0.05766569345994529 0.33927747592906754 chr7 159138663 9628890 0.06050628941126645 0.8507094106552895 chr8 146364022 8665497 0.059205103013635414 0.577790588181678 chr9 141213431 7264569 0.051443895588090344 0.5369258097721927 chr10 135534747 8244598 0.06083014269396172 0.614212367546981 chr11 135006516 7721497 0.05719351353382084 0.4298335657196069 chr12 133851895 7742846 0.05784636818178779 0.2805319308777549 chr13 115169878 5402584 0.04690969630097203 0.24250211624671555 chr14 107349540 5180367 0.04825700231225956 0.29290413466814563 chr15 102531392 4861995 0.04741957468011358 0.2532685604167706 chr16 90354753 4888487 0.05410326338892211 0.33756430822476974 chr17 81195210 4616046 0.056851210804184135 0.3070209194942524 chr18 78077248 4620479 0.05917830249344854 0.9805978092317932 chr19 59128983 3675383 0.062158738634148336 0.8424904224446383 chr20 63025520 3413574 0.05416177446850101 0.28122665403602576 chr21 48129895 2224687 0.04622256084290232 0.2903656028385537 chr22 51304566 1926518 0.03755061489069023 0.2173968444779884 chrMT 16571 12373 0.7466658620481564 0.9758101539524845 chrX 155270560 9875996 0.06360507748539067 0.3531767772101989 chrY 59373566 508954 0.008572063870982584 0.22272891730918237