BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472731.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 = 18,705,414 number of mapped reads = 18,527,769 (99.05%) number of supplementary alignments = 74,229 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,300,774 number of mapped paired reads (second in pair) = 9,226,995 number of mapped paired reads (both in pair) = 18,416,958 number of mapped paired reads (singletons) = 110,811 number of mapped bases = 1,829,820,870 bp number of sequenced bases = 1,829,563,068 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,969,143 duplication rate = 47.59% >>>>>>> Insert size mean insert size = 26,053.2429 std insert size = 1,540,544.4511 median insert size = 248 >>>>>>> Mapping quality mean mapping quality = 55.1694 >>>>>>> ACTG content number of A's = 500,401,848 bp (27.35%) number of C's = 417,162,678 bp (22.8%) number of T's = 497,546,872 bp (27.19%) number of G's = 414,099,728 bp (22.63%) number of N's = 351,942 bp (0.02%) GC percentage = 45.44% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 11,763,700 number of insertions = 103,571 mapped reads with insertion percentage = 0.55% number of deletions = 101,445 mapped reads with deletion percentage = 0.54% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 0.5911X std coverageData = 20.1739X There is a 4.94% of reference with a coverageData >= 1X There is a 2.11% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.47% of reference with a coverageData >= 6X There is a 0.43% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.22% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.21% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% 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 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.18% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 205727006 0.8253821201111471 26.257704454792233 chr2 243199373 116407828 0.47865184257691323 16.006151554246525 chr3 198022430 144527903 0.729856223863125 14.904120832960924 chr4 191154276 50032933 0.2617411132356778 10.778923005933146 chr5 180915260 128152400 0.7083559452088232 23.09932945832576 chr6 171115067 89658264 0.5239647540797795 14.801459223549367 chr7 159138663 44736857 0.2811187184600137 8.504887198315824 chr8 146364022 64367129 0.43977425681838667 15.6942154332549 chr9 141213431 137169283 0.971361449322763 24.51523843853781 chr10 135534747 70781458 0.5222384633218816 26.6111498639673 chr11 135006516 57878280 0.4287073077272804 13.814155569528753 chr12 133851895 109736813 0.8198375749555133 25.024456087281905 chr13 115169878 48151221 0.41808866898339514 17.088247415772447 chr14 107349540 38444221 0.35812189786747106 15.506504348929369 chr15 102531392 61361266 0.5984632101746946 18.493436517144712 chr16 90354753 81182329 0.8984843221252566 23.854723308821267 chr17 81195210 74635634 0.9192122786553542 26.204545102096546 chr18 78077248 47562880 0.609177208704897 33.59682316139086 chr19 59128983 86150733 1.4569966982181988 40.02122940259214 chr20 63025520 53465823 0.8483202201267043 30.302806114480227 chr21 48129895 9315635 0.19355194936535805 7.483114946384009 chr22 51304566 13288560 0.25901320362012226 6.941552148371756 chrMT 16571 4224 0.2549031440468288 0.6843725350081471 chrX 155270560 92715979 0.5971252953554106 15.857699357028611 chrY 59373566 4366211 0.07353796132103636 3.5091988314322093