BamQC report ----------------------------------- >>>>>>> Input bam file = SRR961018.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 = 310,749,478 number of mapped reads = 303,558,512 (97.69%) number of supplementary alignments = 695,503 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 151,952,705 number of mapped paired reads (second in pair) = 151,605,807 number of mapped paired reads (both in pair) = 302,551,870 number of mapped paired reads (singletons) = 1,006,642 number of mapped bases = 29,814,050,877 bp number of sequenced bases = 29,804,785,020 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,039,852 duplication rate = 8.46% >>>>>>> Insert size mean insert size = 21,799.7646 std insert size = 1,374,739.6703 median insert size = 148 >>>>>>> Mapping quality mean mapping quality = 53.663 >>>>>>> ACTG content number of A's = 8,779,402,787 bp (29.46%) number of C's = 6,099,206,576 bp (20.46%) number of T's = 8,757,155,774 bp (29.38%) number of G's = 6,149,642,425 bp (20.63%) number of N's = 19,377,458 bp (0.07%) GC percentage = 41.1% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 145,695,938 number of insertions = 3,075,201 mapped reads with insertion percentage = 0.98% number of deletions = 3,653,403 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.64% >>>>>>> Coverage mean coverageData = 9.6308X std coverageData = 105.7738X There is a 91.44% of reference with a coverageData >= 1X There is a 90.89% of reference with a coverageData >= 2X There is a 89.7% of reference with a coverageData >= 3X There is a 87.5% of reference with a coverageData >= 4X There is a 83.94% of reference with a coverageData >= 5X There is a 78.82% of reference with a coverageData >= 6X There is a 72.18% of reference with a coverageData >= 7X There is a 64.32% of reference with a coverageData >= 8X There is a 55.69% of reference with a coverageData >= 9X There is a 46.81% of reference with a coverageData >= 10X There is a 38.22% of reference with a coverageData >= 11X There is a 30.33% of reference with a coverageData >= 12X There is a 23.42% of reference with a coverageData >= 13X There is a 17.63% of reference with a coverageData >= 14X There is a 12.97% of reference with a coverageData >= 15X There is a 9.34% of reference with a coverageData >= 16X There is a 6.61% of reference with a coverageData >= 17X There is a 4.62% of reference with a coverageData >= 18X There is a 3.2% of reference with a coverageData >= 19X There is a 2.22% of reference with a coverageData >= 20X There is a 1.55% of reference with a coverageData >= 21X There is a 1.1% of reference with a coverageData >= 22X There is a 0.81% of reference with a coverageData >= 23X There is a 0.61% of reference with a coverageData >= 24X There is a 0.49% of reference with a coverageData >= 25X There is a 0.4% of reference with a coverageData >= 26X There is a 0.34% of reference with a coverageData >= 27X There is a 0.3% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.12% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.11% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2426762001 9.736232516748675 251.65428378758685 chr2 243199373 2554177876 10.5024032113767 66.08907923223788 chr3 198022430 1960445723 9.9001195117139 21.40956874280555 chr4 191154276 2006024520 10.494269665199642 93.23577754934907 chr5 180915260 1788658475 9.886719754873083 10.299901367379961 chr6 171115067 1703312485 9.954193484317777 30.65051279416377 chr7 159138663 1591166809 9.998618682626484 64.44916057651564 chr8 146364022 1498113327 10.235529924150349 103.1531716545211 chr9 141213431 1243674256 8.807053601013349 90.53807990015382 chr10 135534747 1560016937 11.510088531024447 249.0843253230438 chr11 135006516 1343537706 9.95165082254252 41.7068761108916 chr12 133851895 1313250791 9.811223001362812 8.125999240526687 chr13 115169878 945436552 8.209060983810367 5.94122579897925 chr14 107349540 877764564 8.176696090174211 9.333801017944605 chr15 102531392 826153579 8.057567179035276 6.091485337607548 chr16 90354753 957853198 10.601027242031197 102.18397162550559 chr17 81195210 799207087 9.843032452283824 39.247550289389864 chr18 78077248 810713556 10.383480165694365 108.13704395391105 chr19 59128983 581586655 9.8358981584378 122.04575115452818 chr20 63025520 614501152 9.75003700088472 34.97432011919763 chr21 48129895 409824142 8.514960234174623 46.494842825755775 chr22 51304566 350128373 6.824507062392848 8.071721414973158 chrMT 16571 22900675 1381.973025164444 196.16321442302907 chrX 155270560 1528721779 9.845535296581657 31.748402697114635 chrY 59373566 100118659 1.6862497192774306 97.8290135504446