BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472494.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 = 18,839,234 number of mapped reads = 18,568,693 (98.56%) number of supplementary alignments = 66,269 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,322,213 number of mapped paired reads (second in pair) = 9,246,480 number of mapped paired reads (both in pair) = 18,430,432 number of mapped paired reads (singletons) = 138,261 number of mapped bases = 1,825,562,396 bp number of sequenced bases = 1,825,313,386 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,534,104 duplication rate = 46.64% >>>>>>> Insert size mean insert size = 28,019.4017 std insert size = 1,675,976.8209 median insert size = 248 >>>>>>> Mapping quality mean mapping quality = 55.0525 >>>>>>> ACTG content number of A's = 506,651,104 bp (27.76%) number of C's = 409,171,825 bp (22.42%) number of T's = 503,138,183 bp (27.56%) number of G's = 406,073,309 bp (22.25%) number of N's = 278,965 bp (0.02%) GC percentage = 44.66% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 11,797,475 number of insertions = 103,862 mapped reads with insertion percentage = 0.55% number of deletions = 98,478 mapped reads with deletion percentage = 0.52% homopolymer indels = 44.81% >>>>>>> Coverage mean coverageData = 0.5897X std coverageData = 17.805X There is a 5.95% of reference with a coverageData >= 1X There is a 2.59% of reference with a coverageData >= 2X There is a 1.11% of reference with a coverageData >= 3X There is a 0.77% of reference with a coverageData >= 4X There is a 0.55% of reference with a coverageData >= 5X There is a 0.48% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.27% 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 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% 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 0.22% 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 0.21% 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 0.2% 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 0.19% 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 0.18% 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 184132175 0.7387430942448886 18.589700787038787 chr2 243199373 139401451 0.5731982335332748 21.825370181087912 chr3 198022430 236495651 1.1942871875675902 25.591157950407453 chr4 191154276 70553880 0.3690939144882116 14.088258894767963 chr5 180915260 101626856 0.5617373349268603 16.54387552281273 chr6 171115067 137894588 0.8058588318233835 20.96511665925653 chr7 159138663 76714629 0.4820615402556197 15.875768698274037 chr8 146364022 67897995 0.46389812244979167 13.47397995150827 chr9 141213431 99971002 0.7079425893985962 16.239613836254442 chr10 135534747 54356921 0.401055243789255 15.623217807898634 chr11 135006516 68740334 0.5091630836544215 13.435387621592271 chr12 133851895 71090925 0.5311163132953777 14.748234604023983 chr13 115169878 44055669 0.38252770398871133 14.928259338958997 chr14 107349540 43293950 0.40329888698172345 19.503225119960614 chr15 102531392 42865537 0.4180723207191023 16.463795464398164 chr16 90354753 51119964 0.565769506336872 13.764073494332667 chr17 81195210 66869518 0.8235648137371651 18.858538171631814 chr18 78077248 28170315 0.36080056254031906 10.569364963441831 chr19 59128983 34685974 0.5866154335852521 15.51145396432208 chr20 63025520 34320631 0.5445513341262397 14.24081742772693 chr21 48129895 7278101 0.15121788651315363 5.693902545075747 chr22 51304566 23064479 0.44955996704075035 13.941862124089766 chrMT 16571 2161 0.13040854504857885 0.5129256067617856 chrX 155270560 137379139 0.8847726123999295 26.439740287671295 chrY 59373566 3580551 0.060305473314504976 2.2557046784879486