BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504599.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 409,492,050 number of mapped reads = 352,316,198 (86.04%) number of supplementary alignments = 1,947,847 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 176,412,959 number of mapped paired reads (second in pair) = 175,903,239 number of mapped paired reads (both in pair) = 350,196,992 number of mapped paired reads (singletons) = 2,119,206 number of mapped bases = 34,975,655,976 bp number of sequenced bases = 34,966,560,223 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,828,233 duplication rate = 21.25% >>>>>>> Insert size mean insert size = 29,791.7866 std insert size = 1,672,309.7336 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.9673 >>>>>>> ACTG content number of A's = 9,227,200,768 bp (26.39%) number of C's = 8,185,010,007 bp (23.41%) number of T's = 9,256,027,364 bp (26.47%) number of G's = 8,293,590,225 bp (23.72%) number of N's = 4,731,859 bp (0.01%) GC percentage = 47.13% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 174,781,559 number of insertions = 2,651,675 mapped reads with insertion percentage = 0.73% number of deletions = 3,552,450 mapped reads with deletion percentage = 0.98% homopolymer indels = 40.54% >>>>>>> Coverage mean coverageData = 11.2982X std coverageData = 23.3668X There is a 78.13% of reference with a coverageData >= 1X There is a 69.32% of reference with a coverageData >= 2X There is a 61.89% of reference with a coverageData >= 3X There is a 55.71% of reference with a coverageData >= 4X There is a 50.4% of reference with a coverageData >= 5X There is a 45.82% of reference with a coverageData >= 6X There is a 41.83% of reference with a coverageData >= 7X There is a 38.32% of reference with a coverageData >= 8X There is a 35.22% of reference with a coverageData >= 9X There is a 32.47% of reference with a coverageData >= 10X There is a 30.01% of reference with a coverageData >= 11X There is a 27.81% of reference with a coverageData >= 12X There is a 25.83% of reference with a coverageData >= 13X There is a 24.04% of reference with a coverageData >= 14X There is a 22.41% of reference with a coverageData >= 15X There is a 20.94% of reference with a coverageData >= 16X There is a 19.59% of reference with a coverageData >= 17X There is a 18.36% of reference with a coverageData >= 18X There is a 17.24% of reference with a coverageData >= 19X There is a 16.21% of reference with a coverageData >= 20X There is a 15.26% of reference with a coverageData >= 21X There is a 14.38% of reference with a coverageData >= 22X There is a 13.57% of reference with a coverageData >= 23X There is a 12.82% of reference with a coverageData >= 24X There is a 12.13% of reference with a coverageData >= 25X There is a 11.49% of reference with a coverageData >= 26X There is a 10.89% of reference with a coverageData >= 27X There is a 10.33% of reference with a coverageData >= 28X There is a 9.81% of reference with a coverageData >= 29X There is a 9.33% of reference with a coverageData >= 30X There is a 8.88% of reference with a coverageData >= 31X There is a 8.45% of reference with a coverageData >= 32X There is a 8.06% of reference with a coverageData >= 33X There is a 7.69% of reference with a coverageData >= 34X There is a 7.34% of reference with a coverageData >= 35X There is a 7.01% of reference with a coverageData >= 36X There is a 6.7% of reference with a coverageData >= 37X There is a 6.41% of reference with a coverageData >= 38X There is a 6.14% of reference with a coverageData >= 39X There is a 5.88% of reference with a coverageData >= 40X There is a 5.64% of reference with a coverageData >= 41X There is a 5.41% of reference with a coverageData >= 42X There is a 5.19% of reference with a coverageData >= 43X There is a 4.98% of reference with a coverageData >= 44X There is a 4.79% of reference with a coverageData >= 45X There is a 4.6% of reference with a coverageData >= 46X There is a 4.42% of reference with a coverageData >= 47X There is a 4.26% of reference with a coverageData >= 48X There is a 4.1% of reference with a coverageData >= 49X There is a 3.95% of reference with a coverageData >= 50X There is a 3.81% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3589125933 14.39966696411962 24.301907086192085 chr2 243199373 2399480474 9.866310280331192 17.62395392195075 chr3 198022430 2590390774 13.0812998002297 21.598719941314435 chr4 191154276 1466964301 7.674242667739224 12.166804991122332 chr5 180915260 1424050875 7.871369584854257 13.22490060840465 chr6 171115067 1788690988 10.453147226363182 17.02574801079879 chr7 159138663 2847049181 17.890367603503115 26.568636965990365 chr8 146364022 2673003895 18.26271141278148 44.894672902901256 chr9 141213431 1374163683 9.731111787801543 19.020996150307493 chr10 135534747 1646067272 12.144983544330518 22.949731620950228 chr11 135006516 1781223989 13.193614958555038 22.29593724596437 chr12 133851895 1192224561 8.907042825206172 14.96704680113316 chr13 115169878 795710100 6.909012267947354 12.9513280294611 chr14 107349540 1168485618 10.884868421420343 18.904917004384924 chr15 102531392 779501333 7.602562666856215 14.192088161116768 chr16 90354753 1019850994 11.287187006089209 19.38143164002961 chr17 81195210 1266872529 15.60279884737043 47.99683644700878 chr18 78077248 458006851 5.866073186903309 27.45209276786086 chr19 59128983 1027120655 17.370849334580978 30.131533924585742 chr20 63025520 1571632116 24.936440286410964 37.19925293368466 chr21 48129895 331988449 6.897759677223481 17.513340139304837 chr22 51304566 717031460 13.975977498766873 26.01804587748211 chrMT 16571 240818 14.532496530082675 12.07772659584853 chrX 155270560 1031472225 6.643063726955065 11.720923000369929 chrY 59373566 35306902 0.594656921903596 14.23485288593157