BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617651.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,684,391 (95.89%) number of supplementary alignments = 142,036 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,374,223 number of mapped paired reads (second in pair) = 15,310,168 number of mapped paired reads (both in pair) = 30,155,548 number of mapped paired reads (singletons) = 528,843 number of mapped bases = 2,990,441,411 bp number of sequenced bases = 2,988,615,041 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,177,040 duplication rate = 10.89% >>>>>>> Insert size mean insert size = 31,069.5408 std insert size = 1,608,422.4405 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 52.738 >>>>>>> ACTG content number of A's = 888,545,219 bp (29.73%) number of C's = 596,868,801 bp (19.97%) number of T's = 887,923,670 bp (29.71%) number of G's = 613,265,822 bp (20.52%) number of N's = 2,011,529 bp (0.07%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.014 number of mismatches = 40,984,779 number of insertions = 465,156 mapped reads with insertion percentage = 1.49% number of deletions = 1,101,830 mapped reads with deletion percentage = 3.52% homopolymer indels = 47.69% >>>>>>> Coverage mean coverageData = 0.966X std coverageData = 10.8823X There is a 33.59% of reference with a coverageData >= 1X There is a 19.55% of reference with a coverageData >= 2X There is a 12.02% of reference with a coverageData >= 3X There is a 7.72% of reference with a coverageData >= 4X There is a 5.1% of reference with a coverageData >= 5X There is a 3.47% of reference with a coverageData >= 6X There is a 2.41% of reference with a coverageData >= 7X There is a 1.72% of reference with a coverageData >= 8X There is a 1.25% of reference with a coverageData >= 9X There is a 0.92% of reference with a coverageData >= 10X There is a 0.69% of reference with a coverageData >= 11X There is a 0.53% of reference with a coverageData >= 12X There is a 0.41% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% 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 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 183357363 0.7356345282686377 10.49563659261971 chr2 243199373 308196087 1.2672569143506798 12.445592780542537 chr3 198022430 250650303 1.2657672315201869 2.5088819588999876 chr4 191154276 166989493 0.8735849204859011 8.76527909444115 chr5 180915260 197972665 1.094283948186571 2.3632360104672183 chr6 171115067 144648582 0.8453293128184908 5.869439953409913 chr7 159138663 233864840 1.469566449731955 13.472917083934613 chr8 146364022 133007098 0.9087417534891191 4.183262821265381 chr9 141213431 122750613 0.8692559350108844 21.34463682736877 chr10 135534747 126756990 0.9352361132898267 21.988067223287008 chr11 135006516 164501813 1.2184731365114259 12.224610976250176 chr12 133851895 127647373 0.9536463641400071 2.167238244206855 chr13 115169878 128916324 1.1193579974097045 2.3326423704997343 chr14 107349540 85375635 0.7953050846794499 2.458663715544762 chr15 102531392 63952816 0.6237388837947309 1.5934864481814475 chr16 90354753 82836539 0.9167922688029483 17.069766993106036 chr17 81195210 73949502 0.9107618786871787 13.161904379141806 chr18 78077248 55206473 0.7070750367635908 18.61517283818396 chr19 59128983 31799380 0.5377968364515926 6.287427747059881 chr20 63025520 81179671 1.288044446122777 3.112019631039627 chr21 48129895 43742530 0.9088432459700982 4.464182441342675 chr22 51304566 19273125 0.3756610084178473 1.2814750577599827 chrMT 16571 3204899 193.40407941584695 137.03306145697192 chrX 155270560 148502018 0.9564080789043332 4.459876244419239 chrY 59373566 12159279 0.20479280291165264 18.04568844373552