BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618649.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 = 66,652,853 number of mapped reads = 63,993,189 (96.01%) number of supplementary alignments = 337,845 (0.51%) number of secondary alignments = 0 number of mapped bases = 6,190,600,134 bp number of sequenced bases = 6,185,142,539 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,966,278 duplication rate = 48.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.4963 >>>>>>> ACTG content number of A's = 1,632,029,657 bp (26.39%) number of C's = 1,439,360,862 bp (23.27%) number of T's = 1,941,682,950 bp (31.39%) number of G's = 1,171,639,972 bp (18.94%) number of N's = 429,098 bp (0.01%) GC percentage = 42.21% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 54,117,913 number of insertions = 1,320,089 mapped reads with insertion percentage = 1.99% number of deletions = 3,028,655 mapped reads with deletion percentage = 4.6% homopolymer indels = 48.32% >>>>>>> Coverage mean coverageData = 1.9997X std coverageData = 44.5192X There is a 13.69% of reference with a coverageData >= 1X There is a 9.16% of reference with a coverageData >= 2X There is a 6.88% of reference with a coverageData >= 3X There is a 5.52% of reference with a coverageData >= 4X There is a 4.64% of reference with a coverageData >= 5X There is a 4.03% of reference with a coverageData >= 6X There is a 3.57% of reference with a coverageData >= 7X There is a 3.21% of reference with a coverageData >= 8X There is a 2.93% of reference with a coverageData >= 9X There is a 2.69% of reference with a coverageData >= 10X There is a 2.5% of reference with a coverageData >= 11X There is a 2.33% of reference with a coverageData >= 12X There is a 2.18% of reference with a coverageData >= 13X There is a 2.05% of reference with a coverageData >= 14X There is a 1.94% of reference with a coverageData >= 15X There is a 1.84% of reference with a coverageData >= 16X There is a 1.74% of reference with a coverageData >= 17X There is a 1.66% of reference with a coverageData >= 18X There is a 1.59% of reference with a coverageData >= 19X There is a 1.52% of reference with a coverageData >= 20X There is a 1.46% of reference with a coverageData >= 21X There is a 1.4% of reference with a coverageData >= 22X There is a 1.34% of reference with a coverageData >= 23X There is a 1.29% of reference with a coverageData >= 24X There is a 1.25% of reference with a coverageData >= 25X There is a 1.2% of reference with a coverageData >= 26X There is a 1.16% of reference with a coverageData >= 27X There is a 1.13% of reference with a coverageData >= 28X There is a 1.09% of reference with a coverageData >= 29X There is a 1.06% of reference with a coverageData >= 30X There is a 1.03% of reference with a coverageData >= 31X There is a 1% of reference with a coverageData >= 32X There is a 0.97% of reference with a coverageData >= 33X There is a 0.94% of reference with a coverageData >= 34X There is a 0.92% of reference with a coverageData >= 35X There is a 0.89% of reference with a coverageData >= 36X There is a 0.87% of reference with a coverageData >= 37X There is a 0.85% of reference with a coverageData >= 38X There is a 0.83% of reference with a coverageData >= 39X There is a 0.81% of reference with a coverageData >= 40X There is a 0.79% of reference with a coverageData >= 41X There is a 0.77% of reference with a coverageData >= 42X There is a 0.75% of reference with a coverageData >= 43X There is a 0.74% of reference with a coverageData >= 44X There is a 0.72% of reference with a coverageData >= 45X There is a 0.7% of reference with a coverageData >= 46X There is a 0.69% of reference with a coverageData >= 47X There is a 0.68% of reference with a coverageData >= 48X There is a 0.66% of reference with a coverageData >= 49X There is a 0.65% of reference with a coverageData >= 50X There is a 0.64% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 570988042 2.290818934408994 44.99538820079366 chr2 243199373 548075468 2.2536055962611385 92.71268344244307 chr3 198022430 407989525 2.0603197577163357 35.76129459859826 chr4 191154276 310734133 1.6255672617022703 37.727006648901146 chr5 180915260 361907574 2.000425912109349 33.59224457136056 chr6 171115067 351026737 2.0514075303491537 31.370625776572293 chr7 159138663 289679067 1.8202934569080802 29.033655584739513 chr8 146364022 317359877 2.168291583296338 37.28560233294517 chr9 141213431 252199161 1.7859431586220718 36.62296744789859 chr10 135534747 294259465 2.1710998213616763 39.994770450435674 chr11 135006516 315330332 2.3356675021522664 38.724658513337445 chr12 133851895 288561220 2.15582468966913 36.38730127415484 chr13 115169878 177901808 1.5446904267798218 32.056039137194375 chr14 107349540 184309668 1.716911576891713 30.892685986468056 chr15 102531392 189873209 1.8518543959687976 29.00268707988188 chr16 90354753 212750167 2.3546095798634963 62.18272214735098 chr17 81195210 167776709 2.066337521634589 34.572992401259675 chr18 78077248 161786659 2.072135777633966 31.140141211670947 chr19 59128983 102413905 1.7320423894319306 28.560817574712217 chr20 63025520 161680686 2.5653209366618475 34.051374937517835 chr21 48129895 66426652 1.3801536861861012 27.98469002155515 chr22 51304566 85517485 1.6668591446617051 52.54937993983167 chrMT 16571 690 0.04163900790537686 0.38726865755967466 chrX 155270560 352295257 2.2689121298976445 33.62436574725219 chrY 59373566 19756638 0.33275141331413377 59.935923963938386