BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173950.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,472,608 number of mapped reads = 3,395,673 (97.78%) number of supplementary alignments = 459,164 (13.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,698,594 number of mapped paired reads (second in pair) = 1,697,079 number of mapped paired reads (both in pair) = 3,345,754 number of mapped paired reads (singletons) = 49,919 number of mapped bases = 386,544,429 bp number of sequenced bases = 386,252,115 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,760,695 duplication rate = 65.65% >>>>>>> Insert size mean insert size = 1,210,052.547 std insert size = 10,156,263.9228 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 52.5823 >>>>>>> ACTG content number of A's = 114,947,375 bp (29.76%) number of C's = 77,018,944 bp (19.94%) number of T's = 113,941,227 bp (29.5%) number of G's = 80,341,661 bp (20.8%) number of N's = 2,908 bp (0%) GC percentage = 40.74% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 3,369,916 number of insertions = 42,263 mapped reads with insertion percentage = 1.19% number of deletions = 126,327 mapped reads with deletion percentage = 3.63% homopolymer indels = 40.19% >>>>>>> Coverage mean coverageData = 0.1249X std coverageData = 2.4052X There is a 2.63% of reference with a coverageData >= 1X There is a 1.99% of reference with a coverageData >= 2X There is a 1.51% of reference with a coverageData >= 3X There is a 1.22% of reference with a coverageData >= 4X There is a 0.92% of reference with a coverageData >= 5X There is a 0.75% of reference with a coverageData >= 6X There is a 0.57% of reference with a coverageData >= 7X There is a 0.49% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.25% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 31938462 0.12813794353595612 1.2953804662266504 chr2 243199373 33674067 0.13846280352046797 7.50612538379261 chr3 198022430 26708380 0.13487552899941688 1.1305768192008465 chr4 191154276 25435214 0.13306118247650395 1.3280588126934925 chr5 180915260 24368283 0.1346944586100697 1.132767315787322 chr6 171115067 22349960 0.13061362971619558 1.1717503922476398 chr7 159138663 21394800 0.13444124511715924 1.3013528736453528 chr8 146364022 19177366 0.131025136764826 1.354035027476186 chr9 141213431 16464437 0.11659257114148017 1.181309030282776 chr10 135534747 19344227 0.14272522307508348 1.5866078655605165 chr11 135006516 17653845 0.13076291073239754 1.1186999665915658 chr12 133851895 17938968 0.1340210237591332 1.133826583852729 chr13 115169878 12581334 0.10924153275563946 1.0146017211948135 chr14 107349540 12038712 0.11214497984807387 1.0230619585900347 chr15 102531392 11065848 0.10792643876326188 0.9949509960092766 chr16 90354753 11930102 0.13203624163523528 1.2319805022156123 chr17 81195210 10841530 0.13352425592593456 1.1300685824614785 chr18 78077248 10611424 0.1359092984424861 1.5212530281900039 chr19 59128983 7398224 0.12512009550375658 1.131857975375687 chr20 63025520 8197564 0.13006737588202366 1.1088245031005817 chr21 48129895 5610858 0.11657739955593088 1.2045474899342044 chr22 51304566 4966775 0.09680960949947418 1.0606914166313242 chrMT 16571 1069363 64.53219479814133 57.72822216753465 chrX 155270560 10826560 0.06972706223253139 0.8149614713031154 chrY 59373566 2958126 0.049822272760238116 0.9296010013659757