BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926998.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 11,262,984 number of mapped reads = 11,037,482 (98%) number of supplementary alignments = 175,954 (1.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,527,341 number of mapped paired reads (second in pair) = 5,510,141 number of mapped paired reads (both in pair) = 10,906,532 number of mapped paired reads (singletons) = 130,950 number of mapped bases = 1,025,843,774 bp number of sequenced bases = 1,025,100,346 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 609,539 duplication rate = 4.86% >>>>>>> Insert size mean insert size = 131,085.4784 std insert size = 3,561,033.1965 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 53.4257 >>>>>>> ACTG content number of A's = 290,095,921 bp (28.3%) number of C's = 206,207,846 bp (20.12%) number of T's = 293,024,410 bp (28.58%) number of G's = 235,571,961 bp (22.98%) number of N's = 200,208 bp (0.02%) GC percentage = 43.1% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 9,232,969 number of insertions = 159,099 mapped reads with insertion percentage = 1.42% number of deletions = 519,183 mapped reads with deletion percentage = 4.58% homopolymer indels = 52.63% >>>>>>> Coverage mean coverageData = 0.3314X std coverageData = 1.0782X There is a 18.59% of reference with a coverageData >= 1X There is a 7.74% of reference with a coverageData >= 2X There is a 3.24% of reference with a coverageData >= 3X There is a 1.56% of reference with a coverageData >= 4X There is a 0.78% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% 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 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 85192517 0.3417946027905784 1.25571648230913 chr2 243199373 87881585 0.3613561331015438 1.5499283147254785 chr3 198022430 68207457 0.34444308657357653 0.8877946637857869 chr4 191154276 58397110 0.3054972727892312 0.9759488518335663 chr5 180915260 60866325 0.3364355499917475 0.8766264105021284 chr6 171115067 58236949 0.34033793762883546 0.9655993693314385 chr7 159138663 52082740 0.32727898436598024 0.9794269165422158 chr8 146364022 59953432 0.409618642483055 1.0566294430375935 chr9 141213431 43331371 0.3068502103032962 1.199090610850704 chr10 135534747 49882412 0.3680415030398072 1.2858810476713127 chr11 135006516 49403933 0.3659373966809128 0.9895511404833032 chr12 133851895 46148009 0.34476918686881497 0.9046807691430101 chr13 115169878 29947865 0.26003209797617394 0.7671493382681184 chr14 107349540 30767530 0.2866107297711755 0.8269815043195594 chr15 102531392 30735207 0.29976387134195936 0.8547894124948346 chr16 90354753 31918961 0.35326266676862034 1.248441701740074 chr17 81195210 27384762 0.3372706591928268 0.9955011775758272 chr18 78077248 26790248 0.3431249011235642 1.241586776550853 chr19 59128983 17664879 0.29875161221697316 1.0069763528434161 chr20 63025520 25566233 0.4056489022224648 1.0329302183683235 chr21 48129895 13128676 0.2727759119358145 1.2877690564655975 chr22 51304566 14048495 0.2738254330033705 0.8539311695753812 chrMT 16571 179268 10.818176332146521 11.097935820423753 chrX 155270560 56501104 0.3638880673837977 0.9436847747308557 chrY 59373566 1626706 0.027397815384711775 0.8820487402780802