BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16328248.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 1,548,702,256 number of mapped reads = 1,513,342,751 (97.72%) number of supplementary alignments = 65,843,635 (4.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 758,334,603 number of mapped paired reads (second in pair) = 755,008,148 number of mapped paired reads (both in pair) = 1,503,384,000 number of mapped paired reads (singletons) = 9,958,751 number of mapped bases = 210,569,649,714 bp number of sequenced bases = 210,391,792,902 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 669,623,579 duplication rate = 39.31% >>>>>>> Insert size mean insert size = 166,476.0352 std insert size = 3,998,599.9616 median insert size = 265 >>>>>>> Mapping quality mean mapping quality = 53.7854 >>>>>>> ACTG content number of A's = 60,390,390,135 bp (28.7%) number of C's = 44,199,269,064 bp (21.01%) number of T's = 59,700,605,133 bp (28.38%) number of G's = 46,097,619,455 bp (21.91%) number of N's = 3,909,115 bp (0%) GC percentage = 42.92% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,627,191,472 number of insertions = 37,498,061 mapped reads with insertion percentage = 2.36% number of deletions = 98,990,504 mapped reads with deletion percentage = 6.28% homopolymer indels = 44.72% >>>>>>> Coverage mean coverageData = 68.0202X std coverageData = 1,524.4578X There is a 91.78% of reference with a coverageData >= 1X There is a 91.7% of reference with a coverageData >= 2X There is a 91.65% of reference with a coverageData >= 3X There is a 91.62% of reference with a coverageData >= 4X There is a 91.59% of reference with a coverageData >= 5X There is a 91.57% of reference with a coverageData >= 6X There is a 91.54% of reference with a coverageData >= 7X There is a 91.52% of reference with a coverageData >= 8X There is a 91.5% of reference with a coverageData >= 9X There is a 91.48% of reference with a coverageData >= 10X There is a 91.46% of reference with a coverageData >= 11X There is a 91.44% of reference with a coverageData >= 12X There is a 91.42% of reference with a coverageData >= 13X There is a 91.4% of reference with a coverageData >= 14X There is a 91.38% of reference with a coverageData >= 15X There is a 91.36% of reference with a coverageData >= 16X There is a 91.33% of reference with a coverageData >= 17X There is a 91.31% of reference with a coverageData >= 18X There is a 91.28% of reference with a coverageData >= 19X There is a 91.25% of reference with a coverageData >= 20X There is a 91.22% of reference with a coverageData >= 21X There is a 91.19% of reference with a coverageData >= 22X There is a 91.15% of reference with a coverageData >= 23X There is a 91.11% of reference with a coverageData >= 24X There is a 91.06% of reference with a coverageData >= 25X There is a 91.01% of reference with a coverageData >= 26X There is a 90.95% of reference with a coverageData >= 27X There is a 90.88% of reference with a coverageData >= 28X There is a 90.81% of reference with a coverageData >= 29X There is a 90.72% of reference with a coverageData >= 30X There is a 90.61% of reference with a coverageData >= 31X There is a 90.49% of reference with a coverageData >= 32X There is a 90.35% of reference with a coverageData >= 33X There is a 90.19% of reference with a coverageData >= 34X There is a 90% of reference with a coverageData >= 35X There is a 89.79% of reference with a coverageData >= 36X There is a 89.53% of reference with a coverageData >= 37X There is a 89.24% of reference with a coverageData >= 38X There is a 88.91% of reference with a coverageData >= 39X There is a 88.53% of reference with a coverageData >= 40X There is a 88.09% of reference with a coverageData >= 41X There is a 87.6% of reference with a coverageData >= 42X There is a 87.04% of reference with a coverageData >= 43X There is a 86.42% of reference with a coverageData >= 44X There is a 85.73% of reference with a coverageData >= 45X There is a 84.95% of reference with a coverageData >= 46X There is a 84.1% of reference with a coverageData >= 47X There is a 83.17% of reference with a coverageData >= 48X There is a 82.15% of reference with a coverageData >= 49X There is a 81.04% of reference with a coverageData >= 50X There is a 79.84% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 17131706966 68.73285569868249 1705.2596012405572 chr2 243199373 18824197938 77.40232923215636 4810.92577399423 chr3 198022430 13658807400 68.97606195419378 69.09674229747179 chr4 191154276 13407731486 70.14089230209007 559.0700003150193 chr5 180915260 12479645324 68.98061182898557 52.11151121542788 chr6 171115067 11924448822 69.68672619577094 288.998069026454 chr7 159138663 11326100651 71.17126936651466 610.233543147079 chr8 146364022 10447593852 71.3808879343313 973.3759289212433 chr9 141213431 9043853050 64.04385890177826 803.2961036734796 chr10 135534747 10940039758 80.71760194454046 1514.3996610154545 chr11 135006516 9518653211 70.50513925564897 269.349543088045 chr12 133851895 9264110660 69.2116511312746 104.07302204977054 chr13 115169878 6445103013 55.961707391927604 38.94072164539338 chr14 107349540 6226999994 58.00676923254632 73.19938220412601 chr15 102531392 5861969734 57.17243879806099 41.890122154256595 chr16 90354753 6441489973 71.29110267171004 302.10184457123046 chr17 81195210 6065050211 74.69714298417357 343.56413425592535 chr18 78077248 5653226399 72.40555403540863 763.5227531598943 chr19 59128983 4513729065 76.33699813507701 928.1151334407849 chr20 63025520 4463456465 70.81982766663408 155.888759641042 chr21 48129895 2862703356 59.47869522674005 241.90561024673488 chr22 51304566 2691677474 52.46467680868795 61.98608756366173 chrMT 16571 380042065 22934.166012914127 3111.362399646047 chrX 155270560 10325418534 66.49952530602066 144.08246131920004 chrY 59373566 671894313 11.31638805390264 607.8493882117733