BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630499.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017516/SRP017516.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 = 95,335,640 number of mapped reads = 95,009,101 (99.66%) number of supplementary alignments = 540,604 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 47,625,255 number of mapped paired reads (second in pair) = 47,383,846 number of mapped paired reads (both in pair) = 94,743,606 number of mapped paired reads (singletons) = 265,495 number of mapped bases = 9,474,395,592 bp number of sequenced bases = 9,472,458,712 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,739,614 duplication rate = 16.09% >>>>>>> Insert size mean insert size = 43,710.1705 std insert size = 1,990,903.2893 median insert size = 319 >>>>>>> Mapping quality mean mapping quality = 54.0031 >>>>>>> ACTG content number of A's = 2,959,297,321 bp (31.24%) number of C's = 1,773,191,728 bp (18.72%) number of T's = 2,944,580,896 bp (31.09%) number of G's = 1,794,595,225 bp (18.95%) number of N's = 793,542 bp (0.01%) GC percentage = 37.66% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 76,589,019 number of insertions = 814,618 mapped reads with insertion percentage = 0.84% number of deletions = 864,441 mapped reads with deletion percentage = 0.89% homopolymer indels = 44.95% >>>>>>> Coverage mean coverageData = 3.0605X std coverageData = 12.1247X There is a 34.15% of reference with a coverageData >= 1X There is a 23.76% of reference with a coverageData >= 2X There is a 18.63% of reference with a coverageData >= 3X There is a 15.41% of reference with a coverageData >= 4X There is a 13.14% of reference with a coverageData >= 5X There is a 11.45% of reference with a coverageData >= 6X There is a 10.12% of reference with a coverageData >= 7X There is a 9.06% of reference with a coverageData >= 8X There is a 8.18% of reference with a coverageData >= 9X There is a 7.45% of reference with a coverageData >= 10X There is a 6.83% of reference with a coverageData >= 11X There is a 6.29% of reference with a coverageData >= 12X There is a 5.82% of reference with a coverageData >= 13X There is a 5.41% of reference with a coverageData >= 14X There is a 5.05% of reference with a coverageData >= 15X There is a 4.72% of reference with a coverageData >= 16X There is a 4.43% of reference with a coverageData >= 17X There is a 4.17% of reference with a coverageData >= 18X There is a 3.93% of reference with a coverageData >= 19X There is a 3.71% of reference with a coverageData >= 20X There is a 3.51% of reference with a coverageData >= 21X There is a 3.33% of reference with a coverageData >= 22X There is a 3.16% of reference with a coverageData >= 23X There is a 3% of reference with a coverageData >= 24X There is a 2.86% of reference with a coverageData >= 25X There is a 2.72% of reference with a coverageData >= 26X There is a 2.6% of reference with a coverageData >= 27X There is a 2.48% of reference with a coverageData >= 28X There is a 2.37% of reference with a coverageData >= 29X There is a 2.27% of reference with a coverageData >= 30X There is a 2.18% of reference with a coverageData >= 31X There is a 2.09% of reference with a coverageData >= 32X There is a 2% of reference with a coverageData >= 33X There is a 1.92% of reference with a coverageData >= 34X There is a 1.85% of reference with a coverageData >= 35X There is a 1.78% of reference with a coverageData >= 36X There is a 1.71% of reference with a coverageData >= 37X There is a 1.65% of reference with a coverageData >= 38X There is a 1.59% of reference with a coverageData >= 39X There is a 1.53% of reference with a coverageData >= 40X There is a 1.48% of reference with a coverageData >= 41X There is a 1.43% of reference with a coverageData >= 42X There is a 1.38% of reference with a coverageData >= 43X There is a 1.33% of reference with a coverageData >= 44X There is a 1.29% of reference with a coverageData >= 45X There is a 1.24% of reference with a coverageData >= 46X There is a 1.2% of reference with a coverageData >= 47X There is a 1.17% of reference with a coverageData >= 48X There is a 1.13% of reference with a coverageData >= 49X There is a 1.09% of reference with a coverageData >= 50X There is a 1.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 762490946 3.059133585869782 12.352827225968332 chr2 243199373 895979748 3.684136751454536 14.829276864275164 chr3 198022430 723632273 3.6542944806807998 12.613646147347001 chr4 191154276 734894460 3.844509656692168 12.768609087748663 chr5 180915260 630572939 3.485460203854556 13.540090889303194 chr6 171115067 653052599 3.8164529310560362 13.809220364980739 chr7 159138663 452915964 2.846046054816987 9.99706721918271 chr8 146364022 470817237 3.2167552556050967 11.68702051250033 chr9 141213431 389323427 2.7569858209875235 11.709764264242134 chr10 135534747 408477189 3.0138189507964332 11.401527857456815 chr11 135006516 421540662 3.1223727156991443 11.848522417188926 chr12 133851895 457194348 3.4156733305867655 11.863073288550567 chr13 115169878 354290289 3.076240898683595 11.781013727842288 chr14 107349540 330665135 3.080265970399128 12.830719239186946 chr15 102531392 248188291 2.420607836866196 13.255478927817073 chr16 90354753 121425156 1.3438712626440361 5.139733967817237 chr17 81195210 148744113 1.8319321176704881 9.086949153945062 chr18 78077248 221472782 2.8365854032150315 8.756600337485558 chr19 59128983 49636232 0.839456886988907 3.9540996753459776 chr20 63025520 135464408 2.1493580378234087 9.092181467885 chr21 48129895 116281303 2.415989126924129 11.085955805327302 chr22 51304566 50550460 0.9853013862352914 7.893568634406117 chrMT 16571 17143 1.0345181340896747 5.564182846873883 chrX 155270560 692178709 4.457887631757108 16.06445396858884 chrY 59373566 4589779 0.07730340805199405 1.0498319564327991