BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038461.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 20,250,000 number of mapped reads = 18,058,744 (89.18%) number of supplementary alignments = 369,174 (1.82%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,188,653 number of mapped paired reads (second in pair) = 8,870,091 number of mapped paired reads (both in pair) = 17,584,570 number of mapped paired reads (singletons) = 474,174 number of mapped bases = 2,353,647,868 bp number of sequenced bases = 2,351,889,458 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,727,851 duplication rate = 18.28% >>>>>>> Insert size mean insert size = 85,843.8262 std insert size = 2,792,567.7701 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 53.171 >>>>>>> ACTG content number of A's = 681,827,554 bp (28.99%) number of C's = 449,166,465 bp (19.1%) number of T's = 700,058,060 bp (29.77%) number of G's = 520,658,394 bp (22.14%) number of N's = 178,985 bp (0.01%) GC percentage = 41.24% >>>>>>> Mismatches and indels general error rate = 0.0136 number of mismatches = 30,733,670 number of insertions = 468,370 mapped reads with insertion percentage = 2.45% number of deletions = 824,973 mapped reads with deletion percentage = 4.38% homopolymer indels = 46.53% >>>>>>> Coverage mean coverageData = 0.7603X std coverageData = 11.1369X There is a 25.25% of reference with a coverageData >= 1X There is a 15.67% of reference with a coverageData >= 2X There is a 9.35% of reference with a coverageData >= 3X There is a 6.26% of reference with a coverageData >= 4X There is a 4.1% of reference with a coverageData >= 5X There is a 2.83% of reference with a coverageData >= 6X There is a 1.96% of reference with a coverageData >= 7X There is a 1.4% of reference with a coverageData >= 8X There is a 1% of reference with a coverageData >= 9X There is a 0.74% of reference with a coverageData >= 10X There is a 0.55% of reference with a coverageData >= 11X There is a 0.41% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.24% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 182197944 0.7309829089653502 15.116243203299707 chr2 243199373 209256178 0.8604305817844358 13.21074645235897 chr3 198022430 153846717 0.7769156100144817 1.979137928789217 chr4 191154276 165586035 0.8662429031930209 11.964257625658954 chr5 180915260 141221549 0.7805950089561268 1.9819441095523969 chr6 171115067 138842852 0.8114005063037494 7.878770730859045 chr7 159138663 124668581 0.7833959306293782 10.802082517418707 chr8 146364022 119136486 0.8139738466602127 4.100371309198954 chr9 141213431 96277933 0.6817901974210937 16.416862487077683 chr10 135534747 129710510 0.9570277207216833 28.636502386451856 chr11 135006516 107067267 0.7930525886617206 6.377600955471819 chr12 133851895 102086258 0.7626807076582667 2.0278153028093815 chr13 115169878 72594638 0.6303266032807641 1.774426133127135 chr14 107349540 67659679 0.6302745125875714 1.9678541421410802 chr15 102531392 61851296 0.6032425269326296 1.6507720160738417 chr16 90354753 74288611 0.8221881919150396 13.16257776287254 chr17 81195210 55716646 0.6862060705305153 10.52734135450564 chr18 78077248 66232368 0.8482928086809617 15.18539409206083 chr19 59128983 32752051 0.5539085798245507 7.761837488975639 chr20 63025520 45688012 0.724912892428337 4.035834252640598 chr21 48129895 30934356 0.6427264385264085 5.6817706404871755 chr22 51304566 20883293 0.4070455054624183 1.7036169697983397 chrMT 16571 7164564 432.35556091967896 354.6558139583731 chrX 155270560 138527568 0.8921689211399766 3.842835018963257 chrY 59373566 9456476 0.15927081085208863 13.791679951843278