BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006063.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 = 10,994,212 number of mapped reads = 9,412,360 (85.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,776,653 number of mapped paired reads (second in pair) = 4,635,707 number of mapped paired reads (both in pair) = 8,531,386 number of mapped paired reads (singletons) = 880,974 number of mapped bases = 362,637,951 bp number of sequenced bases = 362,597,559 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 731,480 duplication rate = 7.1% >>>>>>> Insert size mean insert size = 70,993.5912 std insert size = 2,625,170.4971 median insert size = 95 >>>>>>> Mapping quality mean mapping quality = 46.4935 >>>>>>> ACTG content number of A's = 96,698,168 bp (26.67%) number of C's = 80,456,669 bp (22.19%) number of T's = 99,968,992 bp (27.57%) number of G's = 85,459,230 bp (23.57%) number of N's = 14,500 bp (0%) GC percentage = 45.76% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 2,196,031 number of insertions = 13,153 mapped reads with insertion percentage = 0.14% number of deletions = 32,355 mapped reads with deletion percentage = 0.34% homopolymer indels = 43.96% >>>>>>> Coverage mean coverageData = 0.1171X std coverageData = 0.638X There is a 6.17% of reference with a coverageData >= 1X There is a 2.85% of reference with a coverageData >= 2X There is a 1.32% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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% 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 30888195 0.12392424490689634 0.6948657913592399 chr2 243199373 31040358 0.12763338004165004 0.6991381331164548 chr3 198022430 24698931 0.1247279462230617 0.5828990488209019 chr4 191154276 21862522 0.1143710852693664 0.5784107324783231 chr5 180915260 22047054 0.1218639820654156 0.5808872779142032 chr6 171115067 21009668 0.12278093547425604 0.6639638187496377 chr7 159138663 19800208 0.12442110312312979 0.7460367188813869 chr8 146364022 18324788 0.12520008503182564 0.702896580524462 chr9 141213431 15438889 0.10933017412486777 0.585328706177036 chr10 135534747 17599430 0.12985179365111443 0.6177253400669724 chr11 135006516 16923043 0.1253498238559093 0.867261604217763 chr12 133851895 16638710 0.12430686917058589 0.5897147524818122 chr13 115169878 11239461 0.09759028311204775 0.5214271322147328 chr14 107349540 11068055 0.10310295693861381 0.5416666446819811 chr15 102531392 11173287 0.10897430320657307 0.5581045828841172 chr16 90354753 11847621 0.1311233842894795 0.6498519275979185 chr17 81195210 11365908 0.13998249404121252 0.6823992413300345 chr18 78077248 9407252 0.12048647001492675 0.6840464481346875 chr19 59128983 8377666 0.1416845948458136 0.7779907019980212 chr20 63025520 8510872 0.13503850503732456 0.6269472486191643 chr21 48129895 4888017 0.10155885442924818 0.607516348857206 chr22 51304566 5260686 0.10253835886653831 0.5950998021589318 chrMT 16571 70884 4.2775933860358455 5.385503846041088 chrX 155270560 10843771 0.06983790745650689 0.44617981060146555 chrY 59373566 2312675 0.03895125652382072 0.3561210647979147