BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975246.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 48,835,124 number of mapped reads = 48,775,985 (99.88%) number of supplementary alignments = 279,117 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 24,391,671 number of mapped paired reads (second in pair) = 24,384,314 number of mapped paired reads (both in pair) = 48,756,644 number of mapped paired reads (singletons) = 19,341 number of mapped bases = 4,774,944,144 bp number of sequenced bases = 4,774,462,654 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,499,697 duplication rate = 41.19% >>>>>>> Insert size mean insert size = 57,519.5969 std insert size = 2,361,097.46 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 56.4754 >>>>>>> ACTG content number of A's = 1,132,661,557 bp (23.72%) number of C's = 1,258,935,341 bp (26.37%) number of T's = 1,140,457,461 bp (23.89%) number of G's = 1,242,218,256 bp (26.02%) number of N's = 190,039 bp (0%) GC percentage = 52.39% >>>>>>> Mismatches and indels general error rate = 0.0024 number of mismatches = 10,904,609 number of insertions = 344,025 mapped reads with insertion percentage = 0.7% number of deletions = 218,929 mapped reads with deletion percentage = 0.44% homopolymer indels = 32.19% >>>>>>> Coverage mean coverageData = 1.5424X std coverageData = 15.4131X There is a 7.77% of reference with a coverageData >= 1X There is a 4.57% of reference with a coverageData >= 2X There is a 3.33% of reference with a coverageData >= 3X There is a 2.96% of reference with a coverageData >= 4X There is a 2.7% of reference with a coverageData >= 5X There is a 2.55% of reference with a coverageData >= 6X There is a 2.42% of reference with a coverageData >= 7X There is a 2.32% of reference with a coverageData >= 8X There is a 2.24% of reference with a coverageData >= 9X There is a 2.16% of reference with a coverageData >= 10X There is a 2.1% of reference with a coverageData >= 11X There is a 2.03% of reference with a coverageData >= 12X There is a 1.97% of reference with a coverageData >= 13X There is a 1.92% of reference with a coverageData >= 14X There is a 1.87% of reference with a coverageData >= 15X There is a 1.82% of reference with a coverageData >= 16X There is a 1.77% of reference with a coverageData >= 17X There is a 1.73% of reference with a coverageData >= 18X There is a 1.69% of reference with a coverageData >= 19X There is a 1.65% of reference with a coverageData >= 20X There is a 1.61% of reference with a coverageData >= 21X There is a 1.57% of reference with a coverageData >= 22X There is a 1.54% of reference with a coverageData >= 23X There is a 1.5% of reference with a coverageData >= 24X There is a 1.47% of reference with a coverageData >= 25X There is a 1.44% of reference with a coverageData >= 26X There is a 1.41% of reference with a coverageData >= 27X There is a 1.38% of reference with a coverageData >= 28X There is a 1.35% of reference with a coverageData >= 29X There is a 1.32% of reference with a coverageData >= 30X There is a 1.29% of reference with a coverageData >= 31X There is a 1.27% of reference with a coverageData >= 32X There is a 1.24% of reference with a coverageData >= 33X There is a 1.21% of reference with a coverageData >= 34X There is a 1.19% of reference with a coverageData >= 35X There is a 1.17% of reference with a coverageData >= 36X There is a 1.14% of reference with a coverageData >= 37X There is a 1.12% of reference with a coverageData >= 38X There is a 1.1% of reference with a coverageData >= 39X There is a 1.08% of reference with a coverageData >= 40X There is a 1.06% of reference with a coverageData >= 41X There is a 1.04% of reference with a coverageData >= 42X There is a 1.02% of reference with a coverageData >= 43X There is a 1% of reference with a coverageData >= 44X There is a 0.98% of reference with a coverageData >= 45X There is a 0.96% of reference with a coverageData >= 46X There is a 0.94% of reference with a coverageData >= 47X There is a 0.92% of reference with a coverageData >= 48X There is a 0.91% of reference with a coverageData >= 49X There is a 0.89% of reference with a coverageData >= 50X There is a 0.87% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 408357149 1.638339544999569 14.162194330400238 chr2 243199373 342505587 1.4083325247717642 13.939606510622001 chr3 198022430 226853346 1.1455941935466603 11.30006448132897 chr4 191154276 152104932 0.7957181768719628 9.108823185232914 chr5 180915260 176011632 0.9728954428719833 10.555453153387148 chr6 171115067 213266981 1.2463366595298122 12.812772222868894 chr7 159138663 195782169 1.2302614921428616 12.237040776943132 chr8 146364022 224015724 1.530538181029215 17.732223503091994 chr9 141213431 222203401 1.5735288026533396 15.306761183495418 chr10 135534747 165308681 1.2196774971660957 12.204886521771641 chr11 135006516 356680837 2.64195275582106 21.479488661704437 chr12 133851895 294916061 2.2033013503469636 19.028788480331176 chr13 115169878 61355565 0.5327396891051669 7.0264402040851985 chr14 107349540 156408281 1.4570000113647437 14.09166072994152 chr15 102531392 114057427 1.1124146934433505 10.008244719696336 chr16 90354753 171852904 1.9019796778150675 15.070630073970879 chr17 81195210 313051218 3.8555380052591772 24.76279070801764 chr18 78077248 72881091 0.9334485124270774 11.12785358572435 chr19 59128983 396759687 6.710071218373568 37.32518071269347 chr20 63025520 288379430 4.575597789593803 37.46958822619074 chr21 48129895 37191494 0.7727316670854986 11.095583348651788 chr22 51304566 97586639 1.9021043663053303 14.98744071422042 chrMT 16571 700203 42.25472210488202 55.40649822454244 chrX 155270560 80655735 0.519452850559694 5.9048921583181 chrY 59373566 6057970 0.10203143264125318 2.1802949831935012