BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472526.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 = 15,420,032 number of mapped reads = 15,251,129 (98.9%) number of supplementary alignments = 66,858 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,645,834 number of mapped paired reads (second in pair) = 7,605,295 number of mapped paired reads (both in pair) = 15,166,428 number of mapped paired reads (singletons) = 84,701 number of mapped bases = 1,497,280,352 bp number of sequenced bases = 1,497,082,419 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,413,487 duplication rate = 44.9% >>>>>>> Insert size mean insert size = 31,806.978 std insert size = 1,767,382.3245 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 54.9183 >>>>>>> ACTG content number of A's = 407,210,623 bp (27.2%) number of C's = 343,694,808 bp (22.96%) number of T's = 404,287,000 bp (27%) number of G's = 341,657,243 bp (22.82%) number of N's = 232,745 bp (0.02%) GC percentage = 45.78% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 8,607,354 number of insertions = 82,936 mapped reads with insertion percentage = 0.54% number of deletions = 71,614 mapped reads with deletion percentage = 0.46% homopolymer indels = 44.28% >>>>>>> Coverage mean coverageData = 0.4837X std coverageData = 17.6578X There is a 5% of reference with a coverageData >= 1X There is a 2.26% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 143488004 0.575677618873415 19.66432081137935 chr2 243199373 120115630 0.4938977782644201 18.77913675877169 chr3 198022430 188568865 0.9522601303296804 25.31648863057339 chr4 191154276 55612462 0.2909297304968475 10.859559024110649 chr5 180915260 83047577 0.4590413047522912 19.36083149957221 chr6 171115067 110549261 0.6460521737691282 18.949462310398946 chr7 159138663 65504337 0.41161799254276754 14.254013086963962 chr8 146364022 73091461 0.49938133703376913 26.325277617806254 chr9 141213431 79469433 0.5627611512392189 14.01082117128847 chr10 135534747 37993421 0.2803223663375415 9.506891351626077 chr11 135006516 63660790 0.47153864780867316 14.353537499755323 chr12 133851895 91532783 0.6838362878612962 24.77517687318142 chr13 115169878 25366932 0.22025665426162908 8.149866999216428 chr14 107349540 44865403 0.417937543095201 26.954902932648277 chr15 102531392 42475868 0.4142718358880761 15.193675922519231 chr16 90354753 45920439 0.5082238341130765 17.108159698712434 chr17 81195210 46212391 0.5691516901058572 13.084925141148668 chr18 78077248 27642685 0.3540427680032985 14.1689066319927 chr19 59128983 33519293 0.5668843145839325 15.442339076762714 chr20 63025520 31115477 0.4936964740632049 14.2954424303065 chr21 48129895 5991207 0.12447995159765049 4.392194520684129 chr22 51304566 16399405 0.3196480601746051 11.179235951696876 chrMT 16571 1520 0.09172651016836643 0.401146124017419 chrX 155270560 62481438 0.40240363659408457 11.546888302092176 chrY 59373566 2654270 0.044704574422900586 1.7762737516532403