BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971317.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,024,185 number of mapped reads = 8,359,680 (92.64%) number of supplementary alignments = 1,317 (0.01%) number of secondary alignments = 0 number of mapped bases = 400,558,657 bp number of sequenced bases = 400,473,482 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 758,983 duplication rate = 7.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 35.3566 >>>>>>> ACTG content number of A's = 111,158,659 bp (27.76%) number of C's = 86,578,609 bp (21.62%) number of T's = 113,525,672 bp (28.35%) number of G's = 89,187,668 bp (22.27%) number of N's = 22,874 bp (0.01%) GC percentage = 43.89% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 2,040,343 number of insertions = 26,896 mapped reads with insertion percentage = 0.32% number of deletions = 57,914 mapped reads with deletion percentage = 0.69% homopolymer indels = 39.82% >>>>>>> Coverage mean coverageData = 0.1294X std coverageData = 1.077X There is a 8.66% of reference with a coverageData >= 1X There is a 2.59% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 32581128 0.13071633630954926 1.9783419905031978 chr2 243199373 33568065 0.1380269389099124 1.060793800665822 chr3 198022430 26924073 0.13596476419363202 0.520819045028433 chr4 191154276 26358943 0.1378935567206459 0.76838043682255 chr5 180915260 24072889 0.13306168313275507 0.5159310824715118 chr6 171115067 22926498 0.133982929743995 0.5586363119217292 chr7 159138663 22886569 0.14381526505598455 1.6512911549711264 chr8 146364022 19947498 0.1362868943298101 1.6458146641243245 chr9 141213431 17162868 0.12153849586729466 1.0051585865841943 chr10 135534747 19461712 0.14359204876075063 1.305605007389809 chr11 135006516 18314374 0.13565548199169883 0.8190471909886262 chr12 133851895 18697114 0.139685090001901 0.5529006417399677 chr13 115169878 12430296 0.10793009609682837 0.45591173654998784 chr14 107349540 12075063 0.11248360263118035 0.6225411909969217 chr15 102531392 11867600 0.11574601464495869 0.4818187315460458 chr16 90354753 11648746 0.12892233793168578 0.6396787042584222 chr17 81195210 12371048 0.15236179572661984 0.6627918837315208 chr18 78077248 11813846 0.1513097131702183 1.9088267673530346 chr19 59128983 9554394 0.16158563051896224 1.641878260229678 chr20 63025520 8198438 0.13008124328049972 0.5506826091916914 chr21 48129895 5118225 0.10634191078123066 0.7378471761458941 chr22 51304566 4829973 0.09414314117772675 0.5020752705367634 chrMT 16571 40184 2.4249592661879187 2.770770674956417 chrX 155270560 14167411 0.09124338187483835 0.5305099659550204 chrY 59373566 3541702 0.059651158564402215 0.6965525578409759