BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777254.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 20,849,002 number of mapped reads = 20,684,202 (99.21%) number of supplementary alignments = 836,243 (4.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,344,057 number of mapped paired reads (second in pair) = 10,340,145 number of mapped paired reads (both in pair) = 20,612,336 number of mapped paired reads (singletons) = 71,866 number of mapped bases = 2,047,404,794 bp number of sequenced bases = 2,046,348,821 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,202,335 duplication rate = 31.51% >>>>>>> Insert size mean insert size = 245,421.7513 std insert size = 3,576,507.9635 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 54.5365 >>>>>>> ACTG content number of A's = 560,052,178 bp (27.37%) number of C's = 461,957,329 bp (22.57%) number of T's = 558,469,102 bp (27.29%) number of G's = 465,784,499 bp (22.76%) number of N's = 85,713 bp (0%) GC percentage = 45.34% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 7,200,395 number of insertions = 482,812 mapped reads with insertion percentage = 2.23% number of deletions = 340,435 mapped reads with deletion percentage = 1.48% homopolymer indels = 36.45% >>>>>>> Coverage mean coverageData = 0.6614X std coverageData = 33.3236X There is a 9.97% of reference with a coverageData >= 1X There is a 5% of reference with a coverageData >= 2X There is a 3.1% of reference with a coverageData >= 3X There is a 2.45% of reference with a coverageData >= 4X There is a 2.06% of reference with a coverageData >= 5X There is a 1.83% of reference with a coverageData >= 6X There is a 1.65% of reference with a coverageData >= 7X There is a 1.52% of reference with a coverageData >= 8X There is a 1.4% of reference with a coverageData >= 9X There is a 1.31% of reference with a coverageData >= 10X There is a 1.22% of reference with a coverageData >= 11X There is a 1.15% of reference with a coverageData >= 12X There is a 1.08% of reference with a coverageData >= 13X There is a 1.02% of reference with a coverageData >= 14X There is a 0.96% of reference with a coverageData >= 15X There is a 0.91% of reference with a coverageData >= 16X There is a 0.87% of reference with a coverageData >= 17X There is a 0.82% of reference with a coverageData >= 18X There is a 0.79% of reference with a coverageData >= 19X There is a 0.75% of reference with a coverageData >= 20X There is a 0.71% of reference with a coverageData >= 21X There is a 0.68% of reference with a coverageData >= 22X There is a 0.65% of reference with a coverageData >= 23X There is a 0.63% of reference with a coverageData >= 24X There is a 0.6% of reference with a coverageData >= 25X There is a 0.57% of reference with a coverageData >= 26X There is a 0.55% of reference with a coverageData >= 27X There is a 0.53% of reference with a coverageData >= 28X There is a 0.51% of reference with a coverageData >= 29X There is a 0.49% of reference with a coverageData >= 30X There is a 0.47% of reference with a coverageData >= 31X There is a 0.46% of reference with a coverageData >= 32X There is a 0.44% of reference with a coverageData >= 33X There is a 0.42% of reference with a coverageData >= 34X There is a 0.41% of reference with a coverageData >= 35X There is a 0.39% of reference with a coverageData >= 36X There is a 0.38% of reference with a coverageData >= 37X There is a 0.37% of reference with a coverageData >= 38X There is a 0.36% of reference with a coverageData >= 39X There is a 0.34% of reference with a coverageData >= 40X There is a 0.33% of reference with a coverageData >= 41X There is a 0.32% of reference with a coverageData >= 42X There is a 0.31% of reference with a coverageData >= 43X There is a 0.3% of reference with a coverageData >= 44X There is a 0.29% of reference with a coverageData >= 45X There is a 0.28% of reference with a coverageData >= 46X There is a 0.27% of reference with a coverageData >= 47X There is a 0.27% of reference with a coverageData >= 48X There is a 0.26% of reference with a coverageData >= 49X There is a 0.25% of reference with a coverageData >= 50X There is a 0.24% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 193848538 0.7777253963190728 6.484417345440966 chr2 243199373 174773161 0.7186414950173412 6.34805518205533 chr3 198022430 118424178 0.5980341620896178 5.675506883066345 chr4 191154276 92607114 0.4844626860452758 22.46377354865377 chr5 180915260 97112269 0.5367831823584146 5.07398564176464 chr6 171115067 89018693 0.5202270878928504 5.083845547968101 chr7 159138663 126853212 0.7971237762629688 9.633749226467573 chr8 146364022 66860768 0.4568114970221302 5.20840248593182 chr9 141213431 136641187 0.9676217483873755 151.18612560772988 chr10 135534747 86632025 0.6391868278619357 5.878575841289786 chr11 135006516 136470178 1.010841417461658 8.36393293495385 chr12 133851895 110898967 0.8285199623060996 6.770886367735155 chr13 115169878 55002229 0.47757477871080145 5.19766782420562 chr14 107349540 42209846 0.3932000640151788 4.038338600995608 chr15 102531392 99964699 0.9749667594486574 8.513943818742868 chr16 90354753 60256725 0.6668904844441332 5.4899703946941365 chr17 81195210 82909823 1.021117169350261 7.936312623950356 chr18 78077248 30209967 0.3869240755002021 5.504880757454966 chr19 59128983 98751412 1.6701016487971727 11.869931584826473 chr20 63025520 53265273 0.845138175773877 6.905501657013705 chr21 48129895 13236801 0.2750224366789082 3.4751287900983803 chr22 51304566 21621460 0.42143344512455283 4.027701456757436 chrMT 16571 768289 46.36346629654215 20.9667291686375 chrX 155270560 58096972 0.3741660492497741 4.508495351684296 chrY 59373566 971008 0.01635421392745721 0.820560113235609