BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006094.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 5,136,998 number of mapped reads = 4,555,689 (88.68%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,299,273 number of mapped paired reads (second in pair) = 2,256,416 number of mapped paired reads (both in pair) = 4,244,370 number of mapped paired reads (singletons) = 311,319 number of mapped bases = 176,091,338 bp number of sequenced bases = 176,072,633 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 152,723 duplication rate = 2.98% >>>>>>> Insert size mean insert size = 54,607.7245 std insert size = 2,254,097.9896 median insert size = 94 >>>>>>> Mapping quality mean mapping quality = 47.1062 >>>>>>> ACTG content number of A's = 46,921,169 bp (26.65%) number of C's = 39,613,724 bp (22.5%) number of T's = 48,170,381 bp (27.36%) number of G's = 41,359,899 bp (23.49%) number of N's = 7,460 bp (0%) GC percentage = 45.99% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 803,014 number of insertions = 5,594 mapped reads with insertion percentage = 0.12% number of deletions = 14,539 mapped reads with deletion percentage = 0.32% homopolymer indels = 44.64% >>>>>>> Coverage mean coverageData = 0.0569X std coverageData = 0.3326X There is a 4.31% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% 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% 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 15032892 0.06031235524985914 0.36360787215079843 chr2 243199373 15361175 0.06316288899313897 0.36880459313744524 chr3 198022430 11989346 0.06054539377180656 0.30808969542060577 chr4 191154276 10807479 0.056537992380562806 0.31057459914286867 chr5 180915260 10680972 0.059038535499990434 0.30540069711156065 chr6 171115067 10103347 0.059044169383400937 0.31894737552423985 chr7 159138663 9541916 0.05995975974738458 0.39665922110683416 chr8 146364022 8826004 0.06030173180127559 0.35745779826401197 chr9 141213431 7550264 0.05346703883995284 0.3149218486533915 chr10 135534747 8445253 0.06231061175773619 0.3293773082553816 chr11 135006516 8271987 0.06127102042985837 0.40017229858450265 chr12 133851895 8043688 0.060093941890027036 0.30938483916801895 chr13 115169878 5476275 0.047549542424625994 0.2744106369139007 chr14 107349540 5572130 0.051906417111801315 0.29400170893602395 chr15 102531392 5402517 0.05269134549543617 0.2917313659775765 chr16 90354753 5606479 0.06204963008420819 0.35944672748861833 chr17 81195210 5236631 0.06449433408694921 0.3392098956776107 chr18 78077248 4609249 0.05903447057970076 0.38974880591162964 chr19 59128983 3994715 0.06755933887785623 0.3990888103882553 chr20 63025520 4172087 0.06619678822166006 0.33153665714100494 chr21 48129895 2383288 0.049517830861671316 0.31410602317709274 chr22 51304566 2440449 0.047567871444424654 0.3243958028849112 chrMT 16571 5812 0.35073320861746426 0.8861147554443854 chrX 155270560 5332222 0.0343414875298962 0.2401686227725652 chrY 59373566 1205161 0.020297938648320364 0.21538902288846248