BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975289.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 = 54,349,888 number of mapped reads = 54,214,862 (99.75%) number of supplementary alignments = 98,847 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,105,755 number of mapped paired reads (second in pair) = 27,109,107 number of mapped paired reads (both in pair) = 54,168,262 number of mapped paired reads (singletons) = 46,600 number of mapped bases = 5,011,121,735 bp number of sequenced bases = 5,009,443,556 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,901,001 duplication rate = 47.52% >>>>>>> Insert size mean insert size = 41,093.2582 std insert size = 2,006,800.4783 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 56.0499 >>>>>>> ACTG content number of A's = 1,306,352,601 bp (26.08%) number of C's = 1,101,675,309 bp (21.99%) number of T's = 1,388,620,971 bp (27.72%) number of G's = 1,212,636,028 bp (24.21%) number of N's = 158,647 bp (0%) GC percentage = 46.2% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 32,497,959 number of insertions = 508,758 mapped reads with insertion percentage = 0.93% number of deletions = 1,199,896 mapped reads with deletion percentage = 2.18% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 1.6187X std coverageData = 26.1514X There is a 9.39% of reference with a coverageData >= 1X There is a 4.92% of reference with a coverageData >= 2X There is a 3.02% of reference with a coverageData >= 3X There is a 2.39% of reference with a coverageData >= 4X There is a 2% of reference with a coverageData >= 5X There is a 1.81% of reference with a coverageData >= 6X There is a 1.66% of reference with a coverageData >= 7X There is a 1.57% of reference with a coverageData >= 8X There is a 1.49% of reference with a coverageData >= 9X There is a 1.42% of reference with a coverageData >= 10X There is a 1.37% of reference with a coverageData >= 11X There is a 1.32% of reference with a coverageData >= 12X There is a 1.28% of reference with a coverageData >= 13X There is a 1.24% of reference with a coverageData >= 14X There is a 1.2% of reference with a coverageData >= 15X There is a 1.17% of reference with a coverageData >= 16X There is a 1.14% of reference with a coverageData >= 17X There is a 1.11% of reference with a coverageData >= 18X There is a 1.09% of reference with a coverageData >= 19X There is a 1.06% of reference with a coverageData >= 20X There is a 1.04% of reference with a coverageData >= 21X There is a 1.01% of reference with a coverageData >= 22X There is a 0.99% of reference with a coverageData >= 23X There is a 0.97% of reference with a coverageData >= 24X There is a 0.95% of reference with a coverageData >= 25X There is a 0.93% of reference with a coverageData >= 26X There is a 0.92% of reference with a coverageData >= 27X There is a 0.9% of reference with a coverageData >= 28X There is a 0.88% of reference with a coverageData >= 29X There is a 0.87% of reference with a coverageData >= 30X There is a 0.85% of reference with a coverageData >= 31X There is a 0.84% of reference with a coverageData >= 32X There is a 0.82% of reference with a coverageData >= 33X There is a 0.81% of reference with a coverageData >= 34X There is a 0.8% 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 0.75% of reference with a coverageData >= 39X There is a 0.74% of reference with a coverageData >= 40X There is a 0.73% 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 0.69% of reference with a coverageData >= 44X There is a 0.68% 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 0.63% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 620998229 2.491461110542228 35.8189397137238 chr2 243199373 368146116 1.5137626033271065 23.214203119846413 chr3 198022430 265073560 1.3386037127208266 21.059321528086933 chr4 191154276 220694271 1.1545348376093874 19.49970038379209 chr5 180915260 250298349 1.383511534626764 22.732285012665272 chr6 171115067 380315322 2.222570628453192 34.76729855800596 chr7 159138663 269577838 1.6939807895709165 27.175496735804877 chr8 146364022 182839133 1.2492081763098857 20.886689738030586 chr9 141213431 202628269 1.4349079090076071 23.19751516469875 chr10 135534747 219145695 1.6168967726040024 24.758985542888542 chr11 135006516 250040539 1.8520627478454448 28.102214891485694 chr12 133851895 293804424 2.1949963726699573 30.395645824866588 chr13 115169878 108189731 0.9393925988182431 23.799417857877664 chr14 107349540 167888450 1.5639419600680171 25.07625312586588 chr15 102531392 178670292 1.7425911080969232 26.899852428431227 chr16 90354753 159555756 1.7658811595666695 25.29267728266491 chr17 81195210 200426556 2.4684529543060485 32.598824654857715 chr18 78077248 92006478 1.1784031885959916 21.088700264263057 chr19 59128983 187884643 3.1775388898537287 38.93266709703515 chr20 63025520 127271107 2.01935830120878 29.985194240782217 chr21 48129895 51817911 1.0766263047114482 22.52491695617886 chr22 51304566 82853451 1.614933279037971 25.49359434297614 chrMT 16571 85310 5.148150383199566 9.372355601530712 chrX 155270560 130072152 0.8377129057820104 16.821552150642585 chrY 59373566 838153 0.01411660199085903 0.7758245947037006