BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085012.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,328,184 number of mapped reads = 3,081,272 (92.58%) number of supplementary alignments = 14,422 (0.43%) number of secondary alignments = 0 number of mapped bases = 215,865,104 bp number of sequenced bases = 215,779,334 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,119 duplication rate = 1.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4702 >>>>>>> ACTG content number of A's = 62,535,323 bp (28.98%) number of C's = 43,368,812 bp (20.1%) number of T's = 63,355,858 bp (29.36%) number of G's = 46,510,331 bp (21.55%) number of N's = 9,010 bp (0%) GC percentage = 41.65% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,934,809 number of insertions = 15,561 mapped reads with insertion percentage = 0.5% number of deletions = 47,085 mapped reads with deletion percentage = 1.51% homopolymer indels = 48.3% >>>>>>> Coverage mean coverageData = 0.0697X std coverageData = 0.4978X There is a 5.73% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 18795828 0.07540935274139196 0.8806146227017708 chr2 243199373 20887184 0.08588502405390659 0.5625781433016722 chr3 198022430 12873592 0.06501077680947558 0.3077710454089612 chr4 191154276 12273866 0.06420921496937898 0.31872185272641285 chr5 180915260 10675300 0.05900718380527989 0.2824418607975287 chr6 171115067 14856953 0.08682434142400798 0.48377698861567614 chr7 159138663 19402591 0.12192254625137827 0.6183854980711025 chr8 146364022 12621526 0.08623380136410845 0.6834223008852237 chr9 141213431 7750721 0.05488657095230552 0.4609924956394282 chr10 135534747 15831822 0.11681006052270862 0.6657625961605351 chr11 135006516 8835859 0.06544764846757471 0.4615836702353637 chr12 133851895 8814492 0.06585257534082727 0.3071801532351892 chr13 115169878 4064043 0.03528737783329075 0.21341125641519348 chr14 107349540 7170924 0.06679976458213048 0.32596387534047055 chr15 102531392 3829204 0.03734664989235687 0.22265789161925417 chr16 90354753 6067777 0.0671550394255408 0.33470829002407854 chr17 81195210 3445516 0.04243496629912035 0.2850210569429193 chr18 78077248 5115705 0.06552107215664159 0.8053417648437697 chr19 59128983 3585969 0.06064655297724299 0.5987541054986434 chr20 63025520 5043368 0.0800210454431792 0.335837388573267 chr21 48129895 2394007 0.049740540676434054 0.2909995254950729 chr22 51304566 1533140 0.029883110208943197 0.19814995538565905 chrMT 16571 29688 1.7915635749200411 1.5868022666765211 chrX 155270560 9511836 0.06125975200965334 0.32376616442576034 chrY 59373566 454193 0.007649751069356353 0.1803683278796156