BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472779.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 20,441,498 number of mapped reads = 20,232,233 (98.98%) number of supplementary alignments = 68,621 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,164,085 number of mapped paired reads (second in pair) = 10,068,148 number of mapped paired reads (both in pair) = 20,095,218 number of mapped paired reads (singletons) = 137,015 number of mapped bases = 1,996,738,090 bp number of sequenced bases = 1,996,465,819 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,443,313 duplication rate = 48.46% >>>>>>> Insert size mean insert size = 24,041.6199 std insert size = 1,524,800.9549 median insert size = 267 >>>>>>> Mapping quality mean mapping quality = 55.1323 >>>>>>> ACTG content number of A's = 559,487,477 bp (28.02%) number of C's = 441,956,524 bp (22.14%) number of T's = 555,660,712 bp (27.83%) number of G's = 438,979,332 bp (21.99%) number of N's = 381,774 bp (0.02%) GC percentage = 44.12% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 13,133,595 number of insertions = 119,394 mapped reads with insertion percentage = 0.58% number of deletions = 111,688 mapped reads with deletion percentage = 0.54% homopolymer indels = 45.62% >>>>>>> Coverage mean coverageData = 0.645X std coverageData = 23.1566X There is a 5.25% of reference with a coverageData >= 1X There is a 2.28% of reference with a coverageData >= 2X There is a 1.07% of reference with a coverageData >= 3X There is a 0.75% of reference with a coverageData >= 4X There is a 0.57% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 189585406 0.7606215994141896 28.59754228351933 chr2 243199373 153932211 0.63294657836145 23.303248526174706 chr3 198022430 211054503 1.0658110952380495 23.144147033293446 chr4 191154276 98165248 0.5135393780048112 24.036223607172285 chr5 180915260 100372623 0.5548046251045932 18.582510764734685 chr6 171115067 144938424 0.8470231554770101 23.080767396834197 chr7 159138663 73816238 0.46384854948793935 16.815888902888254 chr8 146364022 76393678 0.5219430086445698 18.205245646039646 chr9 141213431 118472812 0.8389627754317506 19.60115539950088 chr10 135534747 50240086 0.3706804868274849 15.549380724275327 chr11 135006516 136439699 1.0106156579879448 43.02007582850876 chr12 133851895 93230490 0.6965197616365462 22.909511875941245 chr13 115169878 58822871 0.5107487480363572 24.036569425248192 chr14 107349540 40002295 0.3726359237310192 11.19140626775208 chr15 102531392 47649626 0.46473206956948365 14.153620812687445 chr16 90354753 53411982 0.5911363843803547 16.369292191415457 chr17 81195210 63191477 0.7782660701290137 19.15884185013002 chr18 78077248 34951737 0.44765585231692595 16.124655776856695 chr19 59128983 46499596 0.7864095345593886 23.336425331566314 chr20 63025520 48427729 0.7683828550720406 26.273229214333377 chr21 48129895 6875291 0.1428486598609866 4.3386487281945 chr22 51304566 18454539 0.3597055864384468 9.848418518898464 chrMT 16571 3294 0.198781002956973 0.7112642055070592 chrX 155270560 130219794 0.8386637750259933 35.59005616652313 chrY 59373566 1586441 0.026719651637565445 0.8191957450091552