BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472672.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 = 18,426,340 number of mapped reads = 18,290,844 (99.26%) number of supplementary alignments = 143,213 (0.78%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,170,295 number of mapped paired reads (second in pair) = 9,120,549 number of mapped paired reads (both in pair) = 18,200,842 number of mapped paired reads (singletons) = 90,002 number of mapped bases = 1,799,089,812 bp number of sequenced bases = 1,798,859,024 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,197,271 duplication rate = 49.28% >>>>>>> Insert size mean insert size = 21,232.346 std insert size = 1,397,992.1042 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 54.7741 >>>>>>> ACTG content number of A's = 485,057,508 bp (26.96%) number of C's = 417,384,689 bp (23.2%) number of T's = 485,316,715 bp (26.98%) number of G's = 410,766,015 bp (22.83%) number of N's = 334,097 bp (0.02%) GC percentage = 46.04% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 11,017,941 number of insertions = 133,659 mapped reads with insertion percentage = 0.72% number of deletions = 101,199 mapped reads with deletion percentage = 0.54% homopolymer indels = 46.36% >>>>>>> Coverage mean coverageData = 0.5812X std coverageData = 30.6848X There is a 3.48% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.81% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.36% 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 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% 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 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% 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 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% 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 194034485 0.7784714205386072 28.594760963145816 chr2 243199373 119944339 0.4931934549025338 24.474761565009917 chr3 198022430 188063314 0.9497071316618021 29.924202110059497 chr4 191154276 66425881 0.3474987972542137 19.463380300580067 chr5 180915260 77666293 0.429296528109348 23.81447286362448 chr6 171115067 146424782 0.8557094624519535 33.484871941307745 chr7 159138663 62459853 0.39248697847863656 23.597433815030815 chr8 146364022 114583751 0.7828682857594608 33.013262682275 chr9 141213431 87799567 0.6217508234043262 25.018219291629308 chr10 135534747 69034449 0.5093487133598295 30.207760309678903 chr11 135006516 52634321 0.389865041773243 29.310157464868613 chr12 133851895 108994929 0.8142950012026352 32.63885479604552 chr13 115169878 64077047 0.5563698435106443 32.01944706107507 chr14 107349540 53459367 0.49799344272923757 23.036155349691825 chr15 102531392 18697195 0.18235580962365167 8.541303316681745 chr16 90354753 97878423 1.0832681154028498 48.92301202709077 chr17 81195210 90920216 1.119773149179613 79.09100523747378 chr18 78077248 20272441 0.25964594704977306 10.632990327089061 chr19 59128983 72202541 1.2211023653155002 67.61003657525742 chr20 63025520 36704267 0.5823715060185144 27.258428719751738 chr21 48129895 10156780 0.21102850941187384 10.111398284297492 chr22 51304566 14521514 0.28304525566009076 10.542718475031766 chrMT 16571 20226 1.22056604912196 1.4320408930799482 chrX 155270560 29452441 0.18968464466155077 19.36871202395004 chrY 59373566 2661390 0.04482449310859988 3.102017198139662