BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618629.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 = 30,993,522 number of mapped reads = 28,990,835 (93.54%) number of supplementary alignments = 142,019 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,761,137 number of mapped paired reads (second in pair) = 14,229,698 number of mapped paired reads (both in pair) = 28,017,398 number of mapped paired reads (singletons) = 973,437 number of mapped bases = 2,707,373,457 bp number of sequenced bases = 2,705,524,465 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,454,086 duplication rate = 34.37% >>>>>>> Insert size mean insert size = 109,126.7234 std insert size = 3,289,396.3846 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 53.5397 >>>>>>> ACTG content number of A's = 738,330,644 bp (27.29%) number of C's = 587,856,281 bp (21.73%) number of T's = 749,954,306 bp (27.72%) number of G's = 627,500,506 bp (23.19%) number of N's = 1,882,728 bp (0.07%) GC percentage = 44.92% >>>>>>> Mismatches and indels general error rate = 0.0138 number of mismatches = 36,602,876 number of insertions = 512,927 mapped reads with insertion percentage = 1.73% number of deletions = 1,318,878 mapped reads with deletion percentage = 4.44% homopolymer indels = 51.85% >>>>>>> Coverage mean coverageData = 0.8746X std coverageData = 4.5506X There is a 18.02% of reference with a coverageData >= 1X There is a 12.03% of reference with a coverageData >= 2X There is a 8.88% of reference with a coverageData >= 3X There is a 6.94% of reference with a coverageData >= 4X There is a 5.56% of reference with a coverageData >= 5X There is a 4.56% of reference with a coverageData >= 6X There is a 3.79% of reference with a coverageData >= 7X There is a 3.19% of reference with a coverageData >= 8X There is a 2.71% of reference with a coverageData >= 9X There is a 2.32% of reference with a coverageData >= 10X There is a 2% of reference with a coverageData >= 11X There is a 1.73% of reference with a coverageData >= 12X There is a 1.51% of reference with a coverageData >= 13X There is a 1.32% of reference with a coverageData >= 14X There is a 1.16% of reference with a coverageData >= 15X There is a 1.03% of reference with a coverageData >= 16X There is a 0.91% of reference with a coverageData >= 17X There is a 0.81% of reference with a coverageData >= 18X There is a 0.72% of reference with a coverageData >= 19X There is a 0.64% of reference with a coverageData >= 20X There is a 0.57% of reference with a coverageData >= 21X There is a 0.52% of reference with a coverageData >= 22X There is a 0.46% of reference with a coverageData >= 23X There is a 0.42% of reference with a coverageData >= 24X There is a 0.38% of reference with a coverageData >= 25X There is a 0.34% of reference with a coverageData >= 26X There is a 0.31% of reference with a coverageData >= 27X There is a 0.28% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.12% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 229120107 0.9192358521746672 7.147624441525971 chr2 243199373 208502169 0.8573302078373368 5.237155022570652 chr3 198022430 163887432 0.8276205478338994 3.274779525782163 chr4 191154276 129682489 0.6784179340042594 3.112936581054548 chr5 180915260 145710024 0.8054048287579499 3.300288052487957 chr6 171115067 267716913 1.5645431912784162 5.345034485165873 chr7 159138663 127361597 0.8003183802040614 3.4936451055921958 chr8 146364022 121581797 0.8306808964295884 3.3978977047480994 chr9 141213431 111781838 0.7915807810094211 4.123812215738987 chr10 135534747 132419896 0.9770180631244326 3.747766522671694 chr11 135006516 130718501 0.9682384589496407 4.138748531349359 chr12 133851895 120606779 0.9010464812619948 3.974760000036175 chr13 115169878 67624006 0.5871674709944557 2.7536362222864463 chr14 107349540 80849629 0.7531436930237428 3.2541795402850773 chr15 102531392 86383457 0.8425074049516464 3.3761912022195215 chr16 90354753 93116235 1.0305626644787573 10.355384549875701 chr17 81195210 82672342 1.018192353957826 4.04048879018873 chr18 78077248 63776667 0.8168406114928641 3.837584492881384 chr19 59128983 54387502 0.9198112201591562 3.9814192529808756 chr20 63025520 74234863 1.1778540343657617 4.186037367395246 chr21 48129895 31799297 0.6606974106218183 4.555031630628418 chr22 51304566 44183538 0.8612008919440036 3.753225823345775 chrMT 16571 15170 0.9154547100356044 3.3608222617591816 chrX 155270560 134810910 0.8682322650217787 3.3045266940008697 chrY 59373566 4430299 0.07461736423242626 3.024927828232064