BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630579.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 32,519,228 number of mapped reads = 32,044,488 (98.54%) number of supplementary alignments = 67,321 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,087,863 number of mapped paired reads (second in pair) = 15,956,625 number of mapped paired reads (both in pair) = 31,849,184 number of mapped paired reads (singletons) = 195,304 number of mapped bases = 3,115,885,036 bp number of sequenced bases = 3,113,531,015 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,543,627 duplication rate = 6.54% >>>>>>> Insert size mean insert size = 31,550.4002 std insert size = 1,787,071.9868 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 54.0278 >>>>>>> ACTG content number of A's = 897,989,354 bp (28.84%) number of C's = 633,966,482 bp (20.36%) number of T's = 906,448,559 bp (29.11%) number of G's = 674,659,789 bp (21.67%) number of N's = 466,831 bp (0.01%) GC percentage = 42.03% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 27,478,150 number of insertions = 556,878 mapped reads with insertion percentage = 1.71% number of deletions = 1,756,562 mapped reads with deletion percentage = 5.33% homopolymer indels = 54.17% >>>>>>> Coverage mean coverageData = 1.0065X std coverageData = 3.976X There is a 24.75% of reference with a coverageData >= 1X There is a 16.3% of reference with a coverageData >= 2X There is a 11.47% of reference with a coverageData >= 3X There is a 8.55% of reference with a coverageData >= 4X There is a 6.58% of reference with a coverageData >= 5X There is a 5.18% of reference with a coverageData >= 6X There is a 4.15% of reference with a coverageData >= 7X There is a 3.37% of reference with a coverageData >= 8X There is a 2.77% of reference with a coverageData >= 9X There is a 2.3% of reference with a coverageData >= 10X There is a 1.92% of reference with a coverageData >= 11X There is a 1.62% of reference with a coverageData >= 12X There is a 1.37% of reference with a coverageData >= 13X There is a 1.17% of reference with a coverageData >= 14X There is a 1% of reference with a coverageData >= 15X There is a 0.86% of reference with a coverageData >= 16X There is a 0.74% of reference with a coverageData >= 17X There is a 0.65% of reference with a coverageData >= 18X There is a 0.56% of reference with a coverageData >= 19X There is a 0.49% of reference with a coverageData >= 20X There is a 0.43% of reference with a coverageData >= 21X There is a 0.38% of reference with a coverageData >= 22X There is a 0.33% of reference with a coverageData >= 23X There is a 0.29% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.16% of reference with a coverageData >= 29X There is a 0.15% of reference with a coverageData >= 30X There is a 0.13% of reference with a coverageData >= 31X There is a 0.12% of reference with a coverageData >= 32X There is a 0.11% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% 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 257552117 1.0333058187245199 5.709711077577179 chr2 243199373 266272521 1.0948733860428168 5.444340570547067 chr3 198022430 207667655 1.048707739825231 3.0621684694868727 chr4 191154276 183954564 0.9623355953596351 3.420844204450918 chr5 180915260 185961891 1.0278949990177721 3.0368193252624085 chr6 171115067 179556457 1.0493316582110213 3.1997981748680715 chr7 159138663 164065795 1.0309612504410697 3.2076532999008824 chr8 146364022 157685285 1.0773500402988379 3.2577765864269366 chr9 141213431 133414719 0.9447735817707028 4.944628532373127 chr10 135534747 144076469 1.06302237757525 3.474827618548104 chr11 135006516 150661695 1.1159586919493574 4.267871290617033 chr12 133851895 141901050 1.0601347855403915 3.1529737931580346 chr13 115169878 95635682 0.8303879769673803 2.696785254095125 chr14 107349540 93451292 0.870532766139473 2.897347176426852 chr15 102531392 95864493 0.9349769970937291 3.0109855585776963 chr16 90354753 95115590 1.0526904987499661 5.824544800637575 chr17 81195210 83093742 1.0233823152868253 3.5022225274925063 chr18 78077248 83092534 1.0642349228292474 5.137374617514328 chr19 59128983 52043995 0.880177408091054 3.8719669209326395 chr20 63025520 77182676 1.2246257706402106 3.551410580744025 chr21 48129895 39907176 0.829155683801097 3.788982852680186 chr22 51304566 41488445 0.808669641606558 2.987895813637746 chrMT 16571 1746 0.10536479391708406 0.41223467225452637 chrX 155270560 181379287 1.168149886237288 3.4860091117119296 chrY 59373566 4858160 0.08182361827483968 2.7168732840295915