BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006016.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 = 15,674,582 number of mapped reads = 11,365,167 (72.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,720,644 number of mapped paired reads (second in pair) = 5,644,523 number of mapped paired reads (both in pair) = 10,072,904 number of mapped paired reads (singletons) = 1,292,263 number of mapped bases = 439,145,244 bp number of sequenced bases = 439,088,899 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 498,573 duplication rate = 3.66% >>>>>>> Insert size mean insert size = 68,223.9421 std insert size = 2,484,469.5716 median insert size = 108 >>>>>>> Mapping quality mean mapping quality = 47.5639 >>>>>>> ACTG content number of A's = 128,233,862 bp (29.2%) number of C's = 90,955,296 bp (20.71%) number of T's = 127,331,603 bp (29%) number of G's = 92,229,409 bp (21%) number of N's = 338,729 bp (0.08%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 2,927,881 number of insertions = 12,399 mapped reads with insertion percentage = 0.11% number of deletions = 42,720 mapped reads with deletion percentage = 0.38% homopolymer indels = 44.34% >>>>>>> Coverage mean coverageData = 0.1419X std coverageData = 0.8213X There is a 10.32% of reference with a coverageData >= 1X There is a 2.69% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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% 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 35244370 0.14140133275736153 1.1428535903279367 chr2 243199373 36644799 0.1506780159338651 0.6482506525891506 chr3 198022430 31698504 0.16007532076038053 0.5077174774047031 chr4 191154276 30226601 0.1581267321480164 0.5623296301524433 chr5 180915260 27628951 0.1527176369754547 0.49597807033815333 chr6 171115067 25916492 0.15145651668417953 0.6047493110233334 chr7 159138663 24606109 0.1546205588016031 0.9951063789035859 chr8 146364022 23010519 0.1572143118614218 2.3081347145699804 chr9 141213431 18126007 0.1283589448371947 0.5539966639889279 chr10 135534747 20527231 0.15145364162593672 0.7038205203254423 chr11 135006516 20171239 0.1494093736927483 0.5934211804758753 chr12 133851895 19852584 0.14831754156338242 0.4963259848584902 chr13 115169878 14531346 0.1261731474613527 0.4498352786131938 chr14 107349540 13384852 0.12468476343727229 0.48243645797705453 chr15 102531392 12188814 0.11887885029396655 0.4373568990945339 chr16 90354753 11757680 0.13012796349517994 0.5299003700681244 chr17 81195210 11156787 0.13740696033669966 0.5125312958456205 chr18 78077248 11457534 0.14674613019147395 0.8968872604965683 chr19 59128983 7773680 0.13146987493426024 0.8582045231218501 chr20 63025520 8773793 0.13921016439055164 0.49252208603293257 chr21 48129895 5541520 0.11513675647952276 0.4870297044917439 chr22 51304566 4424128 0.08623263668188909 0.3851711558278946 chrMT 16571 44092 2.66079295154185 2.3091477940985943 chrX 155270560 23408073 0.1507566727395071 0.560893201898378 chrY 59373566 1049539 0.017676873240189076 0.3553641381594383