BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618598.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 45,053,364 number of mapped reads = 43,473,764 (96.49%) number of supplementary alignments = 103,001 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,969,532 number of mapped paired reads (second in pair) = 21,504,232 number of mapped paired reads (both in pair) = 42,769,586 number of mapped paired reads (singletons) = 704,178 number of mapped bases = 4,177,956,057 bp number of sequenced bases = 4,174,796,430 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,628,439 duplication rate = 26.8% >>>>>>> Insert size mean insert size = 45,312.5404 std insert size = 2,119,834.6932 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 53.8724 >>>>>>> ACTG content number of A's = 1,090,750,897 bp (26.13%) number of C's = 972,739,732 bp (23.3%) number of T's = 1,093,247,119 bp (26.19%) number of G's = 1,017,831,333 bp (24.38%) number of N's = 227,349 bp (0.01%) GC percentage = 47.68% >>>>>>> Mismatches and indels general error rate = 0.0136 number of mismatches = 55,560,498 number of insertions = 803,065 mapped reads with insertion percentage = 1.81% number of deletions = 2,321,747 mapped reads with deletion percentage = 5.19% homopolymer indels = 52.6% >>>>>>> Coverage mean coverageData = 1.3496X std coverageData = 7.0405X There is a 21.22% of reference with a coverageData >= 1X There is a 14.82% of reference with a coverageData >= 2X There is a 11.22% of reference with a coverageData >= 3X There is a 8.97% of reference with a coverageData >= 4X There is a 7.36% of reference with a coverageData >= 5X There is a 6.18% of reference with a coverageData >= 6X There is a 5.27% of reference with a coverageData >= 7X There is a 4.56% of reference with a coverageData >= 8X There is a 3.98% of reference with a coverageData >= 9X There is a 3.52% of reference with a coverageData >= 10X There is a 3.12% of reference with a coverageData >= 11X There is a 2.8% of reference with a coverageData >= 12X There is a 2.52% of reference with a coverageData >= 13X There is a 2.28% of reference with a coverageData >= 14X There is a 2.07% of reference with a coverageData >= 15X There is a 1.89% of reference with a coverageData >= 16X There is a 1.73% of reference with a coverageData >= 17X There is a 1.59% of reference with a coverageData >= 18X There is a 1.47% of reference with a coverageData >= 19X There is a 1.36% of reference with a coverageData >= 20X There is a 1.26% of reference with a coverageData >= 21X There is a 1.17% of reference with a coverageData >= 22X There is a 1.09% of reference with a coverageData >= 23X There is a 1.02% of reference with a coverageData >= 24X There is a 0.96% of reference with a coverageData >= 25X There is a 0.9% of reference with a coverageData >= 26X There is a 0.84% of reference with a coverageData >= 27X There is a 0.79% of reference with a coverageData >= 28X There is a 0.74% of reference with a coverageData >= 29X There is a 0.7% of reference with a coverageData >= 30X There is a 0.66% of reference with a coverageData >= 31X There is a 0.63% of reference with a coverageData >= 32X There is a 0.59% of reference with a coverageData >= 33X There is a 0.56% of reference with a coverageData >= 34X There is a 0.53% of reference with a coverageData >= 35X There is a 0.51% of reference with a coverageData >= 36X There is a 0.48% of reference with a coverageData >= 37X There is a 0.46% of reference with a coverageData >= 38X There is a 0.43% of reference with a coverageData >= 39X There is a 0.41% of reference with a coverageData >= 40X There is a 0.4% of reference with a coverageData >= 41X There is a 0.38% of reference with a coverageData >= 42X There is a 0.36% of reference with a coverageData >= 43X There is a 0.34% of reference with a coverageData >= 44X There is a 0.33% of reference with a coverageData >= 45X There is a 0.31% of reference with a coverageData >= 46X There is a 0.3% of reference with a coverageData >= 47X There is a 0.29% of reference with a coverageData >= 48X There is a 0.28% of reference with a coverageData >= 49X There is a 0.26% of reference with a coverageData >= 50X There is a 0.25% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 397488065 1.5947324961729985 7.445320520978909 chr2 243199373 328879648 1.3523046706210053 8.086719700782444 chr3 198022430 247171107 1.2481975248965482 5.433095042494889 chr4 191154276 175171542 0.9163882998882013 4.966365677623984 chr5 180915260 215449861 1.1908882700110537 5.189648576842827 chr6 171115067 207947494 1.2152494671904024 5.373408073139095 chr7 159138663 198649710 1.2482806268141138 5.5820280090496315 chr8 146364022 194648972 1.3298963047079972 5.955254035685952 chr9 141213431 185013055 1.3101661342680642 6.9566547919953745 chr10 135534747 213888811 1.5781105268894626 6.5717966376085375 chr11 135006516 223876527 1.6582646055394838 7.184057784943811 chr12 133851895 183028408 1.367394970388727 6.144044352101282 chr13 115169878 94023466 0.8163893861205619 3.883056018156933 chr14 107349540 127249997 1.1853799932444984 5.792806838388268 chr15 102531392 147366987 1.437286514163389 6.711970603852766 chr16 90354753 165368382 1.8302123187697719 16.47329370553832 chr17 81195210 168898567 2.0801543219113543 8.677797725897516 chr18 78077248 98578428 1.262575596926777 6.049860632001307 chr19 59128983 114804664 1.9415971351984864 9.052605993939355 chr20 63025520 134552313 2.1348862016529178 8.018478829182277 chr21 48129895 54640221 1.1352657428402866 10.889540579921304 chr22 51304566 104478180 2.0364304416881724 9.031970591086766 chrMT 16571 30471 1.8388147969344035 6.885121098611916 chrX 155270560 190387826 1.226168218881931 5.051378015339243 chrY 59373566 6363355 0.10717488317949439 5.706678641399037