BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083754.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 = 1,399,251 number of mapped reads = 1,056,655 (75.52%) number of supplementary alignments = 7,076 (0.51%) number of secondary alignments = 0 number of mapped bases = 72,117,029 bp number of sequenced bases = 72,096,364 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,881 duplication rate = 1.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8428 >>>>>>> ACTG content number of A's = 22,674,258 bp (31.45%) number of C's = 13,097,547 bp (18.17%) number of T's = 20,622,926 bp (28.6%) number of G's = 15,690,869 bp (21.76%) number of N's = 10,764 bp (0.01%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 601,290 number of insertions = 4,827 mapped reads with insertion percentage = 0.45% number of deletions = 12,585 mapped reads with deletion percentage = 1.18% homopolymer indels = 44.72% >>>>>>> Coverage mean coverageData = 0.0233X std coverageData = 0.2307X There is a 2.22% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 7606424 0.030517171710476902 0.5006568725411689 chr2 243199373 6265704 0.025763651948230968 0.20982720841646585 chr3 198022430 6157469 0.03109480577528515 0.18166245491642954 chr4 191154276 3516701 0.018397187201818075 0.1390243230574388 chr5 180915260 3517047 0.019440300392570532 0.14283940669465875 chr6 171115067 4947322 0.028912252361739717 0.2076592406381213 chr7 159138663 5012104 0.031495199881125056 0.30564159560010185 chr8 146364022 4920246 0.033616499005472804 0.2664237855829191 chr9 141213431 2856037 0.020224967127949748 0.16803828099427423 chr10 135534747 3201992 0.023624879013497548 0.20830096292771788 chr11 135006516 2624906 0.019442809708532884 0.16451300691888157 chr12 133851895 2531761 0.018914644428455793 0.14143445814943986 chr13 115169878 2311691 0.020072010495661027 0.14415335515699335 chr14 107349540 1539804 0.014343834170132448 0.1255135171086178 chr15 102531392 1785833 0.01741742665504824 0.13535776645445025 chr16 90354753 1883440 0.0208449465851564 0.15764530673607133 chr17 81195210 1369843 0.01687098290650397 0.13830471792546206 chr18 78077248 2053824 0.026305025504997307 0.28883745397827487 chr19 59128983 1745834 0.029525858748492256 0.3014307952941066 chr20 63025520 1456000 0.02310175306764625 0.15648337676983892 chr21 48129895 1129368 0.02346500028724351 0.15921685066135166 chr22 51304566 492198 0.00959364903310945 0.10024463071894896 chrMT 16571 4629 0.27934343129563693 0.5540007745100862 chrX 155270560 3059541 0.0197045788976352 0.14994200799565446 chrY 59373566 127311 0.0021442370498682864 0.06609028050429389