BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975279.sorted.bam outfile = /mainsd/zhouyj/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 = 62,656,372 number of mapped reads = 62,477,314 (99.71%) number of supplementary alignments = 142,689 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 31,262,059 number of mapped paired reads (second in pair) = 31,215,255 number of mapped paired reads (both in pair) = 62,383,292 number of mapped paired reads (singletons) = 94,022 number of mapped bases = 5,707,242,963 bp number of sequenced bases = 5,705,455,259 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,708,851 duplication rate = 43.36% >>>>>>> Insert size mean insert size = 95,997.5328 std insert size = 3,017,156.4773 median insert size = 186 >>>>>>> Mapping quality mean mapping quality = 55.8323 >>>>>>> ACTG content number of A's = 1,546,107,425 bp (27.1%) number of C's = 1,235,724,495 bp (21.66%) number of T's = 1,598,525,971 bp (28.02%) number of G's = 1,324,841,260 bp (23.22%) number of N's = 256,108 bp (0%) GC percentage = 44.88% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 30,105,980 number of insertions = 562,438 mapped reads with insertion percentage = 0.89% number of deletions = 1,129,797 mapped reads with deletion percentage = 1.78% homopolymer indels = 45.94% >>>>>>> Coverage mean coverageData = 1.8436X std coverageData = 22.7575X There is a 15.25% of reference with a coverageData >= 1X There is a 7.8% of reference with a coverageData >= 2X There is a 4.55% of reference with a coverageData >= 3X There is a 3.38% of reference with a coverageData >= 4X There is a 2.69% of reference with a coverageData >= 5X There is a 2.35% of reference with a coverageData >= 6X There is a 2.12% of reference with a coverageData >= 7X There is a 1.97% of reference with a coverageData >= 8X There is a 1.85% of reference with a coverageData >= 9X There is a 1.76% of reference with a coverageData >= 10X There is a 1.68% of reference with a coverageData >= 11X There is a 1.62% of reference with a coverageData >= 12X There is a 1.56% of reference with a coverageData >= 13X There is a 1.51% of reference with a coverageData >= 14X There is a 1.47% of reference with a coverageData >= 15X There is a 1.43% of reference with a coverageData >= 16X There is a 1.39% of reference with a coverageData >= 17X There is a 1.35% of reference with a coverageData >= 18X There is a 1.32% of reference with a coverageData >= 19X There is a 1.29% of reference with a coverageData >= 20X There is a 1.26% of reference with a coverageData >= 21X There is a 1.23% of reference with a coverageData >= 22X There is a 1.2% of reference with a coverageData >= 23X There is a 1.18% of reference with a coverageData >= 24X There is a 1.15% of reference with a coverageData >= 25X There is a 1.13% of reference with a coverageData >= 26X There is a 1.11% of reference with a coverageData >= 27X There is a 1.09% of reference with a coverageData >= 28X There is a 1.07% of reference with a coverageData >= 29X There is a 1.05% of reference with a coverageData >= 30X There is a 1.03% of reference with a coverageData >= 31X There is a 1.01% of reference with a coverageData >= 32X There is a 0.99% of reference with a coverageData >= 33X There is a 0.98% of reference with a coverageData >= 34X There is a 0.96% of reference with a coverageData >= 35X There is a 0.94% of reference with a coverageData >= 36X There is a 0.93% of reference with a coverageData >= 37X There is a 0.91% of reference with a coverageData >= 38X There is a 0.9% of reference with a coverageData >= 39X There is a 0.89% of reference with a coverageData >= 40X There is a 0.87% of reference with a coverageData >= 41X There is a 0.86% of reference with a coverageData >= 42X There is a 0.85% of reference with a coverageData >= 43X There is a 0.83% of reference with a coverageData >= 44X There is a 0.82% of reference with a coverageData >= 45X There is a 0.81% of reference with a coverageData >= 46X There is a 0.8% of reference with a coverageData >= 47X There is a 0.79% of reference with a coverageData >= 48X There is a 0.78% of reference with a coverageData >= 49X There is a 0.77% of reference with a coverageData >= 50X There is a 0.76% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 665158095 2.668631646057163 28.511251922998742 chr2 243199373 410241642 1.686853205826316 20.547636021253137 chr3 198022430 390091578 1.9699363248900643 24.421848932767812 chr4 191154276 285215435 1.4920693429845115 20.58535518817124 chr5 180915260 266886010 1.4751989964804517 18.378008365657955 chr6 171115067 520465253 3.041609731538135 37.37300437506655 chr7 159138663 316549150 1.9891404391150376 25.005885157933058 chr8 146364022 212507167 1.4519084956547585 18.264427296675258 chr9 141213431 230343866 1.6311753377056606 20.081685607262934 chr10 135534747 260306608 1.9205894706838536 22.965729807421912 chr11 135006516 248051568 1.837330340411125 21.22504195720044 chr12 133851895 280523595 2.0957760441120388 21.78817055965514 chr13 115169878 118929173 1.0326413040048545 16.76904922796202 chr14 107349540 186327484 1.735708266658618 20.40861768157133 chr15 102531392 199180220 1.94262670304915 22.006468514441117 chr16 90354753 155039744 1.7159002581745755 19.306233228385597 chr17 81195210 204072210 2.513352819704512 24.56714349710155 chr18 78077248 109042373 1.396596009633946 19.153877681030437 chr19 59128983 226980679 3.8387380855172157 34.10647922428463 chr20 63025520 124662369 1.9779665284792574 23.057437393728918 chr21 48129895 58324643 1.2118173746275573 16.727723644780454 chr22 51304566 76703040 1.4950528964614962 18.004194814009484 chrMT 16571 201045 12.132339629473176 20.72673277080927 chrX 155270560 143828580 0.9263094046933301 12.329181355789414 chrY 59373566 17611436 0.2966208228085879 6.329464006975423