BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618606.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 = 44,822,476 number of mapped reads = 43,137,706 (96.24%) number of supplementary alignments = 132,317 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,736,498 number of mapped paired reads (second in pair) = 21,401,208 number of mapped paired reads (both in pair) = 42,416,442 number of mapped paired reads (singletons) = 721,264 number of mapped bases = 4,057,065,747 bp number of sequenced bases = 4,054,225,619 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,372,854 duplication rate = 18.71% >>>>>>> Insert size mean insert size = 63,259.8355 std insert size = 2,508,772.4727 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 53.2329 >>>>>>> ACTG content number of A's = 1,103,725,242 bp (27.22%) number of C's = 879,043,476 bp (21.68%) number of T's = 1,119,910,536 bp (27.62%) number of G's = 951,227,103 bp (23.46%) number of N's = 319,262 bp (0.01%) GC percentage = 45.14% >>>>>>> Mismatches and indels general error rate = 0.0117 number of mismatches = 46,195,329 number of insertions = 726,402 mapped reads with insertion percentage = 1.66% number of deletions = 2,079,939 mapped reads with deletion percentage = 4.7% homopolymer indels = 53.09% >>>>>>> Coverage mean coverageData = 1.3106X std coverageData = 4.8255X There is a 27.97% of reference with a coverageData >= 1X There is a 18.69% of reference with a coverageData >= 2X There is a 13.51% of reference with a coverageData >= 3X There is a 10.42% of reference with a coverageData >= 4X There is a 8.25% of reference with a coverageData >= 5X There is a 6.71% of reference with a coverageData >= 6X There is a 5.53% of reference with a coverageData >= 7X There is a 4.63% of reference with a coverageData >= 8X There is a 3.92% of reference with a coverageData >= 9X There is a 3.35% of reference with a coverageData >= 10X There is a 2.88% of reference with a coverageData >= 11X There is a 2.5% of reference with a coverageData >= 12X There is a 2.18% of reference with a coverageData >= 13X There is a 1.91% of reference with a coverageData >= 14X There is a 1.68% of reference with a coverageData >= 15X There is a 1.48% of reference with a coverageData >= 16X There is a 1.32% of reference with a coverageData >= 17X There is a 1.17% of reference with a coverageData >= 18X There is a 1.05% of reference with a coverageData >= 19X There is a 0.94% of reference with a coverageData >= 20X There is a 0.84% of reference with a coverageData >= 21X There is a 0.76% of reference with a coverageData >= 22X There is a 0.68% of reference with a coverageData >= 23X There is a 0.62% of reference with a coverageData >= 24X There is a 0.56% of reference with a coverageData >= 25X There is a 0.51% of reference with a coverageData >= 26X There is a 0.46% of reference with a coverageData >= 27X There is a 0.42% of reference with a coverageData >= 28X There is a 0.39% of reference with a coverageData >= 29X There is a 0.35% of reference with a coverageData >= 30X There is a 0.32% of reference with a coverageData >= 31X There is a 0.3% of reference with a coverageData >= 32X There is a 0.27% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.13% of reference with a coverageData >= 42X There is a 0.12% of reference with a coverageData >= 43X There is a 0.12% of reference with a coverageData >= 44X There is a 0.11% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.09% of reference with a coverageData >= 47X There is a 0.09% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 366801352 1.4716166023112938 5.404229426016797 chr2 243199373 347399689 1.4284563513245572 5.751171533512033 chr3 198022430 271109409 1.3690843456471067 3.960528755049205 chr4 191154276 211729271 1.107635546693185 3.924886884653021 chr5 180915260 239912348 1.326103436492864 3.9549405191539684 chr6 171115067 225834100 1.3197791635730125 4.083656447438034 chr7 159138663 209700990 1.3177249704554825 4.074863647502051 chr8 146364022 207751722 1.419417963247826 4.279235509615386 chr9 141213431 184631398 1.3074634380918058 5.590309099948877 chr10 135534747 210309227 1.5516997054637214 4.55584989038243 chr11 135006516 214538594 1.5890980699035298 5.614213473463929 chr12 133851895 192131781 1.4354057594776675 4.293722842294717 chr13 115169878 112022197 0.9726692338772817 3.211314866487511 chr14 107349540 132734912 1.2364739709178074 4.348793995445786 chr15 102531392 139078329 1.3564463164608163 4.205741700429406 chr16 90354753 147544133 1.6329426853726223 9.390265309745603 chr17 81195210 138831332 1.709846332068111 5.064454772615346 chr18 78077248 104095579 1.3332383205924472 5.532086040550628 chr19 59128983 94858916 1.6042710560403177 5.25723337054295 chr20 63025520 120498113 1.911893991513279 5.318465170942458 chr21 48129895 55851590 1.160434486715585 6.126260003537773 chr22 51304566 75268611 1.4670938060366792 4.967501231857213 chrMT 16571 330297 19.93223100597429 62.374521869007076 chrX 155270560 17012134 0.10956445317129017 1.3957683225231585 chrY 59373566 37089723 0.624684106054873 4.230058608816288