BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21671990.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 299,983,516 number of mapped reads = 298,549,094 (99.52%) number of supplementary alignments = 1,279,015 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 149,307,363 number of mapped paired reads (second in pair) = 149,241,731 number of mapped paired reads (both in pair) = 298,021,140 number of mapped paired reads (singletons) = 527,954 number of mapped bases = 44,303,005,196 bp number of sequenced bases = 44,285,150,889 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,074,898 duplication rate = 21.52% >>>>>>> Insert size mean insert size = 75,506.5268 std insert size = 2,650,567.2245 median insert size = 346 >>>>>>> Mapping quality mean mapping quality = 54.5589 >>>>>>> ACTG content number of A's = 12,966,135,106 bp (29.28%) number of C's = 9,203,078,297 bp (20.78%) number of T's = 12,887,154,337 bp (29.1%) number of G's = 9,228,406,428 bp (20.84%) number of N's = 376,721 bp (0%) GC percentage = 41.62% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 257,276,749 number of insertions = 5,959,861 mapped reads with insertion percentage = 1.89% number of deletions = 6,510,727 mapped reads with deletion percentage = 2.09% homopolymer indels = 45.79% >>>>>>> Coverage mean coverageData = 14.3112X std coverageData = 149.0137X There is a 92.25% of reference with a coverageData >= 1X There is a 92.08% of reference with a coverageData >= 2X There is a 91.76% of reference with a coverageData >= 3X There is a 91.19% of reference with a coverageData >= 4X There is a 90.28% of reference with a coverageData >= 5X There is a 88.93% of reference with a coverageData >= 6X There is a 87.01% of reference with a coverageData >= 7X There is a 84.4% of reference with a coverageData >= 8X There is a 81% of reference with a coverageData >= 9X There is a 76.74% of reference with a coverageData >= 10X There is a 71.62% of reference with a coverageData >= 11X There is a 65.72% of reference with a coverageData >= 12X There is a 59.24% of reference with a coverageData >= 13X There is a 52.39% of reference with a coverageData >= 14X There is a 45.44% of reference with a coverageData >= 15X There is a 38.65% of reference with a coverageData >= 16X There is a 32.24% of reference with a coverageData >= 17X There is a 26.4% of reference with a coverageData >= 18X There is a 21.23% of reference with a coverageData >= 19X There is a 16.79% of reference with a coverageData >= 20X There is a 13.08% of reference with a coverageData >= 21X There is a 10.05% of reference with a coverageData >= 22X There is a 7.63% of reference with a coverageData >= 23X There is a 5.75% of reference with a coverageData >= 24X There is a 4.3% of reference with a coverageData >= 25X There is a 3.22% of reference with a coverageData >= 26X There is a 2.41% of reference with a coverageData >= 27X There is a 1.82% of reference with a coverageData >= 28X There is a 1.4% of reference with a coverageData >= 29X There is a 1.1% of reference with a coverageData >= 30X There is a 0.88% of reference with a coverageData >= 31X There is a 0.72% of reference with a coverageData >= 32X There is a 0.61% of reference with a coverageData >= 33X There is a 0.54% of reference with a coverageData >= 34X There is a 0.48% of reference with a coverageData >= 35X There is a 0.43% of reference with a coverageData >= 36X There is a 0.4% of reference with a coverageData >= 37X There is a 0.37% of reference with a coverageData >= 38X There is a 0.35% of reference with a coverageData >= 39X There is a 0.33% of reference with a coverageData >= 40X There is a 0.32% of reference with a coverageData >= 41X There is a 0.3% of reference with a coverageData >= 42X There is a 0.29% of reference with a coverageData >= 43X There is a 0.28% of reference with a coverageData >= 44X There is a 0.27% of reference with a coverageData >= 45X There is a 0.26% of reference with a coverageData >= 46X There is a 0.25% of reference with a coverageData >= 47X There is a 0.24% of reference with a coverageData >= 48X There is a 0.23% of reference with a coverageData >= 49X There is a 0.23% of reference with a coverageData >= 50X There is a 0.22% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3707735041 14.875529802591746 371.00685207343565 chr2 243199373 3842970877 15.801730200184357 97.21508078167088 chr3 198022430 2927436419 14.783357718618037 9.067032779709168 chr4 191154276 2885623519 15.095783256242722 79.4298263639508 chr5 180915260 2663877913 14.72445117675535 11.07954905830839 chr6 171115067 2586845450 15.1175784538015 96.90474582755625 chr7 159138663 2422555450 15.222921974655524 105.44864685488366 chr8 146364022 2234253145 15.265043379308064 128.08820753114787 chr9 141213431 1977206096 14.001544201556861 262.4871679278971 chr10 135534747 2256040453 16.645476550747535 233.0020427449391 chr11 135006516 2055671911 15.226464410058549 64.13093738966903 chr12 133851895 1976749662 14.768185851982148 11.799878898137274 chr13 115169878 1412939800 12.268310295509734 8.583335927807754 chr14 107349540 1347795711 12.555207139220158 10.975662862934882 chr15 102531392 1274507053 12.43040817196747 8.724656966815882 chr16 90354753 1437578589 15.9103814826432 91.99434301913948 chr17 81195210 1306760079 16.094053811795057 84.84789511221541 chr18 78077248 1251511792 16.029148363425925 205.65580524955232 chr19 59128983 951495456 16.09186236130596 169.11442976023525 chr20 63025520 958994047 15.21596405709941 32.09790180927818 chr21 48129895 634971530 13.192871706867425 51.18601057655078 chr22 51304566 590768228 11.514924967886873 41.7887272165924 chrMT 16571 23612965 1424.9571540643292 147.5784564180711 chrX 155270560 1174148486 7.561951769865453 23.465743874367053 chrY 59373566 400955524 6.753098239037891 105.68553705947218