BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975285.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 59,449,350 number of mapped reads = 59,340,998 (99.82%) number of supplementary alignments = 59,904 (0.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 29,665,535 number of mapped paired reads (second in pair) = 29,675,463 number of mapped paired reads (both in pair) = 59,300,296 number of mapped paired reads (singletons) = 40,702 number of mapped bases = 5,576,028,312 bp number of sequenced bases = 5,574,532,310 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,982,523 duplication rate = 49.05% >>>>>>> Insert size mean insert size = 59,293.4219 std insert size = 2,406,100.1005 median insert size = 191 >>>>>>> Mapping quality mean mapping quality = 56.3933 >>>>>>> ACTG content number of A's = 1,453,595,946 bp (26.08%) number of C's = 1,263,367,261 bp (22.66%) number of T's = 1,500,028,422 bp (26.91%) number of G's = 1,357,362,072 bp (24.35%) number of N's = 178,609 bp (0%) GC percentage = 47.01% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 32,169,460 number of insertions = 457,161 mapped reads with insertion percentage = 0.76% number of deletions = 1,101,606 mapped reads with deletion percentage = 1.84% homopolymer indels = 49.05% >>>>>>> Coverage mean coverageData = 1.8012X std coverageData = 32.6068X There is a 8.98% of reference with a coverageData >= 1X There is a 4.7% of reference with a coverageData >= 2X There is a 2.93% of reference with a coverageData >= 3X There is a 2.32% of reference with a coverageData >= 4X There is a 1.95% of reference with a coverageData >= 5X There is a 1.76% of reference with a coverageData >= 6X There is a 1.62% of reference with a coverageData >= 7X There is a 1.53% of reference with a coverageData >= 8X There is a 1.45% of reference with a coverageData >= 9X There is a 1.39% of reference with a coverageData >= 10X There is a 1.33% of reference with a coverageData >= 11X There is a 1.29% of reference with a coverageData >= 12X There is a 1.25% of reference with a coverageData >= 13X There is a 1.21% of reference with a coverageData >= 14X There is a 1.17% of reference with a coverageData >= 15X There is a 1.14% of reference with a coverageData >= 16X There is a 1.11% of reference with a coverageData >= 17X There is a 1.09% of reference with a coverageData >= 18X There is a 1.06% of reference with a coverageData >= 19X There is a 1.04% of reference with a coverageData >= 20X There is a 1.01% of reference with a coverageData >= 21X There is a 0.99% of reference with a coverageData >= 22X There is a 0.97% of reference with a coverageData >= 23X There is a 0.95% of reference with a coverageData >= 24X There is a 0.94% of reference with a coverageData >= 25X There is a 0.92% of reference with a coverageData >= 26X There is a 0.9% of reference with a coverageData >= 27X There is a 0.89% of reference with a coverageData >= 28X There is a 0.87% of reference with a coverageData >= 29X There is a 0.86% of reference with a coverageData >= 30X There is a 0.84% of reference with a coverageData >= 31X There is a 0.83% of reference with a coverageData >= 32X There is a 0.82% of reference with a coverageData >= 33X There is a 0.8% of reference with a coverageData >= 34X There is a 0.79% of reference with a coverageData >= 35X There is a 0.78% of reference with a coverageData >= 36X There is a 0.77% of reference with a coverageData >= 37X There is a 0.76% of reference with a coverageData >= 38X There is a 0.74% of reference with a coverageData >= 39X There is a 0.73% of reference with a coverageData >= 40X There is a 0.72% of reference with a coverageData >= 41X There is a 0.71% of reference with a coverageData >= 42X There is a 0.7% of reference with a coverageData >= 43X There is a 0.7% of reference with a coverageData >= 44X There is a 0.69% of reference with a coverageData >= 45X There is a 0.68% of reference with a coverageData >= 46X There is a 0.67% of reference with a coverageData >= 47X There is a 0.66% of reference with a coverageData >= 48X There is a 0.65% of reference with a coverageData >= 49X There is a 0.64% of reference with a coverageData >= 50X There is a 0.64% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 684757655 2.747265592569978 43.41591154477539 chr2 243199373 374301799 1.5390738651287559 25.615580985477 chr3 198022430 392636086 1.982785919756666 34.464633848847846 chr4 191154276 229356487 1.1998501514033617 24.1611484884244 chr5 180915260 256120349 1.4156923467926366 26.203025921156975 chr6 171115067 510111144 2.9811001038266256 56.65975247207428 chr7 159138663 287507311 1.8066465155610865 35.0652582494163 chr8 146364022 172591019 1.1791901906057214 22.069643576738482 chr9 141213431 214884407 1.5216994975499178 27.001154358069627 chr10 135534747 252017318 1.8594295822900677 33.562629202231896 chr11 135006516 249157277 1.845520382142148 30.30810414374068 chr12 133851895 304357385 2.273836952401757 32.97923849160934 chr13 115169878 101001557 0.8769789354122611 21.399546128628778 chr14 107349540 198702650 1.8509874378595381 31.573137838680843 chr15 102531392 188557833 1.8390253884390841 28.15050519102701 chr16 90354753 184871639 2.0460643503723595 33.17208539721719 chr17 81195210 209935988 2.585571094649549 36.808495894735245 chr18 78077248 98291490 1.2589005442404937 25.217291810175823 chr19 59128983 218885376 3.7018288645350115 46.8358670663522 chr20 63025520 145203427 2.303883046105768 36.03289086914279 chr21 48129895 54593601 1.1342971140909408 24.88692179092233 chr22 51304566 102985845 2.007342679791892 31.887541645677633 chrMT 16571 29315 1.76905437209583 5.734252556542817 chrX 155270560 138692219 0.8932293346530082 18.57759353983065 chrY 59373566 6479135 0.10912490922307075 3.7084618466745916