BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472416.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 = 14,935,924 number of mapped reads = 14,811,266 (99.17%) number of supplementary alignments = 53,302 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,425,836 number of mapped paired reads (second in pair) = 7,385,430 number of mapped paired reads (both in pair) = 14,738,212 number of mapped paired reads (singletons) = 73,054 number of mapped bases = 1,447,817,375 bp number of sequenced bases = 1,447,654,942 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,910,960 duplication rate = 46.81% >>>>>>> Insert size mean insert size = 16,713.8839 std insert size = 1,295,031.4594 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 55.0508 >>>>>>> ACTG content number of A's = 387,281,198 bp (26.75%) number of C's = 337,679,461 bp (23.33%) number of T's = 387,875,875 bp (26.79%) number of G's = 334,636,447 bp (23.12%) number of N's = 181,961 bp (0.01%) GC percentage = 46.44% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 7,708,331 number of insertions = 81,936 mapped reads with insertion percentage = 0.55% number of deletions = 70,100 mapped reads with deletion percentage = 0.47% homopolymer indels = 45.82% >>>>>>> Coverage mean coverageData = 0.4677X std coverageData = 14.3399X There is a 4.16% of reference with a coverageData >= 1X There is a 1.86% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 180541801 0.7243384200033748 20.29781485285138 chr2 243199373 97662711 0.40157468251367573 13.115255128417987 chr3 198022430 135940458 0.6864902021452822 16.790460490964993 chr4 191154276 52924322 0.2768670578941169 11.5751227438654 chr5 180915260 69827963 0.3859705532855548 12.916281263141546 chr6 171115067 121432836 0.7096560117642943 16.80816285067596 chr7 159138663 63552704 0.3993542662853715 12.160765693904109 chr8 146364022 67793635 0.4631851056948954 11.696847008837292 chr9 141213431 74894607 0.5303646152468315 15.495680414290991 chr10 135534747 43802993 0.3231864445801489 12.278973798423708 chr11 135006516 64794259 0.47993430924474784 18.374214039149486 chr12 133851895 60387880 0.4511544644175564 11.412327832367085 chr13 115169878 27741862 0.2408777579846008 8.121760778304632 chr14 107349540 39393458 0.3669643856880989 11.68913202996629 chr15 102531392 29049235 0.28332040005854986 8.196200246256875 chr16 90354753 69254688 0.7664753175740517 19.22088435441625 chr17 81195210 69901959 0.8609123493861276 19.42154706651434 chr18 78077248 15228551 0.19504466909489432 5.632638116126198 chr19 59128983 38631871 0.6533491536629338 14.15274881182419 chr20 63025520 23888944 0.37903604762007514 9.971789735840217 chr21 48129895 11157645 0.23182358906039582 10.741905153248352 chr22 51304566 24511030 0.47775533273198334 13.3247289334851 chrMT 16571 1944 0.11731337879427917 0.3834062460414356 chrX 155270560 63667732 0.4100438099791744 16.554624064463727 chrY 59373566 1832287 0.03086031585167042 1.3401473709778011