BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006255.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 = 3,306,982 number of mapped reads = 2,507,295 (75.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,264,281 number of mapped paired reads (second in pair) = 1,243,014 number of mapped paired reads (both in pair) = 2,318,570 number of mapped paired reads (singletons) = 188,725 number of mapped bases = 96,902,402 bp number of sequenced bases = 96,890,142 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,121 duplication rate = 2.76% >>>>>>> Insert size mean insert size = 82,965.9985 std insert size = 2,800,506.4592 median insert size = 130 >>>>>>> Mapping quality mean mapping quality = 47.4223 >>>>>>> ACTG content number of A's = 26,266,133 bp (27.11%) number of C's = 21,661,232 bp (22.36%) number of T's = 26,806,732 bp (27.67%) number of G's = 22,152,057 bp (22.86%) number of N's = 3,988 bp (0%) GC percentage = 45.22% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 389,877 number of insertions = 2,668 mapped reads with insertion percentage = 0.11% number of deletions = 9,112 mapped reads with deletion percentage = 0.36% homopolymer indels = 42.72% >>>>>>> Coverage mean coverageData = 0.0313X std coverageData = 0.2196X There is a 2.76% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 8032968 0.03222847737659197 0.24771075094654277 chr2 243199373 8153099 0.03352434218652365 0.22167519001978145 chr3 198022430 6444645 0.03254502532869635 0.19843891488345358 chr4 191154276 5866207 0.030688337832421808 0.2066668399798096 chr5 180915260 5624509 0.031089190596746787 0.19903039959341157 chr6 171115067 5397909 0.03154549213366465 0.20197089146166924 chr7 159138663 5176428 0.03252778364739686 0.22770576105366194 chr8 146364022 4668728 0.03189805757045949 0.33812875552781885 chr9 141213431 3956392 0.02801710837264481 0.19279390843445884 chr10 135534747 4710180 0.0347525642262054 0.24511325774255985 chr11 135006516 4488148 0.03324393616675509 0.20998818200220323 chr12 133851895 4363545 0.03259979995053488 0.1996493849185501 chr13 115169878 2811559 0.02441227731438597 0.17394598714410872 chr14 107349540 2989494 0.02784822366262585 0.20614139761208627 chr15 102531392 2869282 0.027984424516542213 0.18412551853485454 chr16 90354753 3129359 0.03463413817311858 0.2209553174569761 chr17 81195210 2968528 0.0365603833033993 0.2153560419691867 chr18 78077248 2470910 0.031646991451338036 0.24365752352785963 chr19 59128983 2296793 0.03884377649451539 0.2470135488063179 chr20 63025520 2253820 0.03576043482068851 0.21330357348678372 chr21 48129895 1297160 0.026951232700590765 0.19864235049759346 chr22 51304566 1473899 0.028728417661695062 0.19490699089375632 chrMT 16571 2370 0.14302094019672923 0.5626004290412983 chrX 155270560 5184343 0.033389091918004286 0.20552391109301954 chrY 59373566 272127 0.004583302272934053 0.12584046647412572