BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1778457.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 436,478,520 number of mapped reads = 423,668,252 (97.07%) number of supplementary alignments = 1,587,887 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 213,075,550 number of mapped paired reads (second in pair) = 210,592,702 number of mapped paired reads (both in pair) = 418,184,404 number of mapped paired reads (singletons) = 5,483,848 number of mapped bases = 33,462,666,083 bp number of sequenced bases = 33,453,392,516 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,929,043 duplication rate = 9.64% >>>>>>> Insert size mean insert size = 123,485.6247 std insert size = 3,382,158.7917 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 52.5767 >>>>>>> ACTG content number of A's = 9,492,629,845 bp (28.38%) number of C's = 7,224,056,699 bp (21.59%) number of T's = 9,450,348,073 bp (28.25%) number of G's = 7,276,972,227 bp (21.75%) number of N's = 9,385,672 bp (0.03%) GC percentage = 43.35% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 172,829,395 number of insertions = 3,389,190 mapped reads with insertion percentage = 0.78% number of deletions = 4,138,757 mapped reads with deletion percentage = 0.96% homopolymer indels = 42.26% >>>>>>> Coverage mean coverageData = 10.8094X std coverageData = 117.1384X There is a 92.22% of reference with a coverageData >= 1X There is a 91.65% of reference with a coverageData >= 2X There is a 90.39% of reference with a coverageData >= 3X There is a 88.13% of reference with a coverageData >= 4X There is a 84.69% of reference with a coverageData >= 5X There is a 80.05% of reference with a coverageData >= 6X There is a 74.33% of reference with a coverageData >= 7X There is a 67.8% of reference with a coverageData >= 8X There is a 60.77% of reference with a coverageData >= 9X There is a 53.55% of reference with a coverageData >= 10X There is a 46.4% of reference with a coverageData >= 11X There is a 39.52% of reference with a coverageData >= 12X There is a 33.09% of reference with a coverageData >= 13X There is a 27.21% of reference with a coverageData >= 14X There is a 21.97% of reference with a coverageData >= 15X There is a 17.41% of reference with a coverageData >= 16X There is a 13.54% of reference with a coverageData >= 17X There is a 10.34% of reference with a coverageData >= 18X There is a 7.76% of reference with a coverageData >= 19X There is a 5.75% of reference with a coverageData >= 20X There is a 4.2% of reference with a coverageData >= 21X There is a 3.05% of reference with a coverageData >= 22X There is a 2.21% of reference with a coverageData >= 23X There is a 1.61% of reference with a coverageData >= 24X There is a 1.19% of reference with a coverageData >= 25X There is a 0.9% of reference with a coverageData >= 26X There is a 0.71% of reference with a coverageData >= 27X There is a 0.57% of reference with a coverageData >= 28X There is a 0.48% of reference with a coverageData >= 29X There is a 0.41% of reference with a coverageData >= 30X There is a 0.37% of reference with a coverageData >= 31X There is a 0.33% of reference with a coverageData >= 32X There is a 0.31% of reference with a coverageData >= 33X There is a 0.29% of reference with a coverageData >= 34X There is a 0.27% of reference with a coverageData >= 35X There is a 0.25% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.22% 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 0.19% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2831843139 11.361428620071523 288.1651326463753 chr2 243199373 2863394326 11.773855708090169 79.1350117697237 chr3 198022430 2151702037 10.86595107938025 20.733989349992367 chr4 191154276 2106610956 11.020475189370076 70.7097710525899 chr5 180915260 1958305320 10.824434157737716 13.050779342556106 chr6 171115067 1877262667 10.970761955170202 49.49988839257889 chr7 159138663 1844946630 11.593327449282391 107.23996527619077 chr8 146364022 1665309098 11.377858269021878 107.26160888962154 chr9 141213431 1440343228 10.199760871187953 94.89621812799602 chr10 135534747 1820031167 13.428520783677708 257.7758372069285 chr11 135006516 1558401060 11.543154405969561 57.425793300293186 chr12 133851895 1492218475 11.148280530507245 13.092021414266393 chr13 115169878 1008486515 8.756512835760754 8.572412818400872 chr14 107349540 1014949168 9.4546205600881 14.385518809838901 chr15 102531392 977941629 9.537972809342138 7.676937825027186 chr16 90354753 1117788772 12.371112032147328 56.44067622522735 chr17 81195210 1044653245 12.865946710403238 50.48518433529546 chr18 78077248 899114856 11.51570885285301 137.73995450006325 chr19 59128983 823956622 13.934902651716502 159.29449582992865 chr20 63025520 757210005 12.014339667487075 22.998001355718635 chr21 48129895 474801514 9.86500207407475 55.4899471701355 chr22 51304566 487249846 9.49720237376143 36.8240804831858 chrMT 16571 10942517 660.3413795184358 114.15663614610482 chrX 155270560 883733797 5.691573450884701 25.792891211006676 chrY 59373566 351469494 5.919629183128397 102.32880006199237