BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16352029.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 = 1,630,933,214 number of mapped reads = 1,584,553,489 (97.16%) number of supplementary alignments = 38,228,138 (2.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 793,733,390 number of mapped paired reads (second in pair) = 790,820,099 number of mapped paired reads (both in pair) = 1,569,480,450 number of mapped paired reads (singletons) = 15,073,039 number of mapped bases = 143,145,581,244 bp number of sequenced bases = 143,055,403,791 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 618,975,524 duplication rate = 35.39% >>>>>>> Insert size mean insert size = 165,747.8452 std insert size = 3,990,753.436 median insert size = 281 >>>>>>> Mapping quality mean mapping quality = 52.8861 >>>>>>> ACTG content number of A's = 41,362,151,013 bp (28.91%) number of C's = 29,909,683,103 bp (20.91%) number of T's = 40,946,778,143 bp (28.62%) number of G's = 30,833,837,044 bp (21.55%) number of N's = 2,954,488 bp (0%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,080,219,773 number of insertions = 18,411,998 mapped reads with insertion percentage = 1.14% number of deletions = 59,101,560 mapped reads with deletion percentage = 3.65% homopolymer indels = 45.15% >>>>>>> Coverage mean coverageData = 46.2402X std coverageData = 401.4303X There is a 91.81% of reference with a coverageData >= 1X There is a 91.74% of reference with a coverageData >= 2X There is a 91.7% of reference with a coverageData >= 3X There is a 91.67% of reference with a coverageData >= 4X There is a 91.64% of reference with a coverageData >= 5X There is a 91.62% of reference with a coverageData >= 6X There is a 91.6% of reference with a coverageData >= 7X There is a 91.58% of reference with a coverageData >= 8X There is a 91.55% of reference with a coverageData >= 9X There is a 91.53% of reference with a coverageData >= 10X There is a 91.5% of reference with a coverageData >= 11X There is a 91.48% of reference with a coverageData >= 12X There is a 91.44% of reference with a coverageData >= 13X There is a 91.41% of reference with a coverageData >= 14X There is a 91.36% of reference with a coverageData >= 15X There is a 91.31% of reference with a coverageData >= 16X There is a 91.25% of reference with a coverageData >= 17X There is a 91.17% of reference with a coverageData >= 18X There is a 91.07% of reference with a coverageData >= 19X There is a 90.95% of reference with a coverageData >= 20X There is a 90.79% of reference with a coverageData >= 21X There is a 90.59% of reference with a coverageData >= 22X There is a 90.34% of reference with a coverageData >= 23X There is a 90.02% of reference with a coverageData >= 24X There is a 89.63% of reference with a coverageData >= 25X There is a 89.14% of reference with a coverageData >= 26X There is a 88.54% of reference with a coverageData >= 27X There is a 87.82% of reference with a coverageData >= 28X There is a 86.97% of reference with a coverageData >= 29X There is a 85.97% of reference with a coverageData >= 30X There is a 84.8% of reference with a coverageData >= 31X There is a 83.47% of reference with a coverageData >= 32X There is a 81.97% of reference with a coverageData >= 33X There is a 80.29% of reference with a coverageData >= 34X There is a 78.43% of reference with a coverageData >= 35X There is a 76.4% of reference with a coverageData >= 36X There is a 74.21% of reference with a coverageData >= 37X There is a 71.86% of reference with a coverageData >= 38X There is a 69.36% of reference with a coverageData >= 39X There is a 66.74% of reference with a coverageData >= 40X There is a 64.02% of reference with a coverageData >= 41X There is a 61.2% of reference with a coverageData >= 42X There is a 58.31% of reference with a coverageData >= 43X There is a 55.38% of reference with a coverageData >= 44X There is a 52.42% of reference with a coverageData >= 45X There is a 49.45% of reference with a coverageData >= 46X There is a 46.5% of reference with a coverageData >= 47X There is a 43.58% of reference with a coverageData >= 48X There is a 40.71% of reference with a coverageData >= 49X There is a 37.92% of reference with a coverageData >= 50X There is a 35.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11878249796 47.655848351928476 897.1064782164764 chr2 243199373 12139938590 49.91763934358499 505.9348907339986 chr3 198022430 9331463397 47.123264758441756 37.72717062613874 chr4 191154276 8998929576 47.07678930499049 273.31530134557 chr5 180915260 8542083524 47.215937030408604 32.98514696574009 chr6 171115067 7698899630 44.99252909154984 103.55409166212533 chr7 159138663 7683974364 48.284773914432094 263.83124527522233 chr8 146364022 7058597690 48.22631677885977 556.0393723206585 chr9 141213431 6113391762 43.29185771288285 275.43125353881726 chr10 135534747 7413741596 54.69993311752004 814.3791207136165 chr11 135006516 6515444124 48.26021970672882 156.00819169167988 chr12 133851895 6419231764 47.957720464099516 45.59163017827967 chr13 115169878 4384902000 38.07334066985814 28.93970137858999 chr14 107349540 4285933613 39.92503007465146 44.823885775719155 chr15 102531392 4155231548 40.52643260709851 31.253311014443355 chr16 90354753 4707672112 52.102097075070304 337.48269285936146 chr17 81195210 4268516399 52.57103712152478 159.44200397337045 chr18 78077248 3817509989 48.89401313171284 511.9019342537684 chr19 59128983 3176441349 53.72054765426965 371.2541986885863 chr20 63025520 3130451877 49.66959220645859 55.30881249893904 chr21 48129895 1928460725 40.067835697543075 98.21500443927026 chr22 51304566 1922760416 37.47737415808176 40.54077055767814 chrMT 16571 422924892 25521.989741113994 6211.409991408423 chrX 155270560 6693444972 43.10826838004577 75.29653054139762 chrY 59373566 457385539 7.703521445890583 272.18058328735896