BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975319.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 = 34,466,882 number of mapped reads = 34,259,917 (99.4%) number of supplementary alignments = 81,570 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,177,969 number of mapped paired reads (second in pair) = 17,081,948 number of mapped paired reads (both in pair) = 34,095,808 number of mapped paired reads (singletons) = 164,109 number of mapped bases = 3,171,638,262 bp number of sequenced bases = 3,170,411,945 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,392,781 duplication rate = 56.89% >>>>>>> Insert size mean insert size = 178,810.0764 std insert size = 4,135,292.8819 median insert size = 234 >>>>>>> Mapping quality mean mapping quality = 55.9097 >>>>>>> ACTG content number of A's = 881,656,518 bp (27.81%) number of C's = 652,855,969 bp (20.59%) number of T's = 916,368,282 bp (28.9%) number of G's = 718,843,279 bp (22.67%) number of N's = 687,897 bp (0.02%) GC percentage = 43.27% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 23,752,990 number of insertions = 301,038 mapped reads with insertion percentage = 0.87% number of deletions = 801,739 mapped reads with deletion percentage = 2.29% homopolymer indels = 48.62% >>>>>>> Coverage mean coverageData = 1.0245X std coverageData = 15.4489X There is a 7.86% of reference with a coverageData >= 1X There is a 4.88% of reference with a coverageData >= 2X There is a 2.79% of reference with a coverageData >= 3X There is a 2.18% of reference with a coverageData >= 4X There is a 1.79% of reference with a coverageData >= 5X There is a 1.61% of reference with a coverageData >= 6X There is a 1.47% of reference with a coverageData >= 7X There is a 1.38% of reference with a coverageData >= 8X There is a 1.3% of reference with a coverageData >= 9X There is a 1.24% of reference with a coverageData >= 10X There is a 1.18% of reference with a coverageData >= 11X There is a 1.14% of reference with a coverageData >= 12X There is a 1.09% of reference with a coverageData >= 13X There is a 1.05% of reference with a coverageData >= 14X There is a 1.02% of reference with a coverageData >= 15X There is a 0.98% of reference with a coverageData >= 16X There is a 0.95% of reference with a coverageData >= 17X There is a 0.92% of reference with a coverageData >= 18X There is a 0.89% of reference with a coverageData >= 19X There is a 0.87% of reference with a coverageData >= 20X There is a 0.84% of reference with a coverageData >= 21X There is a 0.82% of reference with a coverageData >= 22X There is a 0.8% of reference with a coverageData >= 23X There is a 0.78% of reference with a coverageData >= 24X There is a 0.76% of reference with a coverageData >= 25X There is a 0.74% of reference with a coverageData >= 26X There is a 0.72% of reference with a coverageData >= 27X There is a 0.71% of reference with a coverageData >= 28X There is a 0.69% of reference with a coverageData >= 29X There is a 0.68% of reference with a coverageData >= 30X There is a 0.66% of reference with a coverageData >= 31X There is a 0.65% of reference with a coverageData >= 32X There is a 0.63% of reference with a coverageData >= 33X There is a 0.62% of reference with a coverageData >= 34X There is a 0.61% of reference with a coverageData >= 35X There is a 0.59% of reference with a coverageData >= 36X There is a 0.58% of reference with a coverageData >= 37X There is a 0.57% of reference with a coverageData >= 38X There is a 0.56% of reference with a coverageData >= 39X There is a 0.55% of reference with a coverageData >= 40X There is a 0.54% of reference with a coverageData >= 41X There is a 0.53% of reference with a coverageData >= 42X There is a 0.52% of reference with a coverageData >= 43X There is a 0.51% of reference with a coverageData >= 44X There is a 0.5% of reference with a coverageData >= 45X There is a 0.49% of reference with a coverageData >= 46X There is a 0.48% of reference with a coverageData >= 47X There is a 0.48% of reference with a coverageData >= 48X There is a 0.47% of reference with a coverageData >= 49X There is a 0.46% of reference with a coverageData >= 50X There is a 0.45% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 322183590 1.292608976087566 17.09691307053217 chr2 243199373 274330933 1.1280083892321549 15.625789546447493 chr3 198022430 216888105 1.0952703943689612 15.611268106909362 chr4 191154276 167879328 0.8782399824527075 13.689356814127216 chr5 180915260 167935604 0.9282556043088902 15.109664422454111 chr6 171115067 199384552 1.1652074565707298 18.36119820812273 chr7 159138663 160985877 1.011607575212568 15.507684222873126 chr8 146364022 127379575 0.8702929398865522 13.054732220651223 chr9 141213431 126168408 0.8934589798331577 13.6402457193727 chr10 135534747 149073755 1.0998932620577364 15.936649843782767 chr11 135006516 176228316 1.3053319293122119 17.016383797443645 chr12 133851895 179405394 1.340327636003958 17.099061058512245 chr13 115169878 78030197 0.6775226157659037 12.636967396429226 chr14 107349540 109982924 1.0245309295223808 15.470902944761047 chr15 102531392 111993921 1.0922890913253183 15.43126075090226 chr16 90354753 86701637 0.9595691883524932 13.415150779884714 chr17 81195210 122276556 1.5059577529265582 19.56783127143698 chr18 78077248 60574000 0.7758214019018703 11.940678893656798 chr19 59128983 108484727 1.83471322346268 28.211665734706198 chr20 63025520 68070710 1.0800499543676911 16.942907214024014 chr21 48129895 31350977 0.6513826178095755 12.016365828328821 chr22 51304566 38641110 0.7531709750746162 12.003119161938606 chrMT 16571 58765 3.5462555066079293 9.056524444224028 chrX 155270560 79123384 0.5095839417337066 9.494481403109022 chrY 59373566 8505917 0.1432610094532641 3.383297958334054