BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618601.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 = 44,638,376 number of mapped reads = 43,071,438 (96.49%) number of supplementary alignments = 141,407 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,750,740 number of mapped paired reads (second in pair) = 21,320,698 number of mapped paired reads (both in pair) = 42,265,594 number of mapped paired reads (singletons) = 805,844 number of mapped bases = 4,071,622,573 bp number of sequenced bases = 4,068,811,575 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,205,930 duplication rate = 18.64% >>>>>>> Insert size mean insert size = 63,749.0691 std insert size = 2,509,133.2395 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 53.6494 >>>>>>> ACTG content number of A's = 1,120,888,935 bp (27.55%) number of C's = 878,495,951 bp (21.59%) number of T's = 1,132,512,150 bp (27.83%) number of G's = 936,711,423 bp (23.02%) number of N's = 203,116 bp (0%) GC percentage = 44.61% >>>>>>> Mismatches and indels general error rate = 0.0127 number of mismatches = 50,694,285 number of insertions = 733,795 mapped reads with insertion percentage = 1.68% number of deletions = 2,056,902 mapped reads with deletion percentage = 4.65% homopolymer indels = 52.82% >>>>>>> Coverage mean coverageData = 1.3153X std coverageData = 5.1827X There is a 25.04% of reference with a coverageData >= 1X There is a 17.15% of reference with a coverageData >= 2X There is a 12.71% of reference with a coverageData >= 3X There is a 9.98% of reference with a coverageData >= 4X There is a 8.05% of reference with a coverageData >= 5X There is a 6.65% of reference with a coverageData >= 6X There is a 5.59% of reference with a coverageData >= 7X There is a 4.75% of reference with a coverageData >= 8X There is a 4.08% of reference with a coverageData >= 9X There is a 3.54% of reference with a coverageData >= 10X There is a 3.09% of reference with a coverageData >= 11X There is a 2.71% of reference with a coverageData >= 12X There is a 2.4% of reference with a coverageData >= 13X There is a 2.13% of reference with a coverageData >= 14X There is a 1.9% of reference with a coverageData >= 15X There is a 1.7% of reference with a coverageData >= 16X There is a 1.52% of reference with a coverageData >= 17X There is a 1.37% of reference with a coverageData >= 18X There is a 1.24% of reference with a coverageData >= 19X There is a 1.12% of reference with a coverageData >= 20X There is a 1.02% of reference with a coverageData >= 21X There is a 0.93% of reference with a coverageData >= 22X There is a 0.85% of reference with a coverageData >= 23X There is a 0.77% of reference with a coverageData >= 24X There is a 0.71% of reference with a coverageData >= 25X There is a 0.65% of reference with a coverageData >= 26X There is a 0.6% of reference with a coverageData >= 27X There is a 0.55% of reference with a coverageData >= 28X There is a 0.51% of reference with a coverageData >= 29X There is a 0.47% of reference with a coverageData >= 30X There is a 0.43% of reference with a coverageData >= 31X There is a 0.4% of reference with a coverageData >= 32X There is a 0.37% of reference with a coverageData >= 33X There is a 0.34% of reference with a coverageData >= 34X There is a 0.32% of reference with a coverageData >= 35X There is a 0.3% of reference with a coverageData >= 36X There is a 0.28% of reference with a coverageData >= 37X There is a 0.26% of reference with a coverageData >= 38X There is a 0.24% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 358797524 1.439505035375619 5.772201949160297 chr2 243199373 342660473 1.4089693931900062 6.0918906831187165 chr3 198022430 262489838 1.3255560897823544 4.373054354757612 chr4 191154276 208338620 1.0898977745075396 4.316871127052626 chr5 180915260 237888748 1.314918089275609 4.370415195519171 chr6 171115067 221968442 1.2971881780579848 4.519832289689061 chr7 159138663 205707388 1.2926298620467862 4.316984925237995 chr8 146364022 199676086 1.3642429558269449 4.496299122267493 chr9 141213431 176840416 1.2522917596981267 5.296508619666677 chr10 135534747 203064464 1.498246527143331 4.932975410358795 chr11 135006516 199473851 1.4775127668652674 6.023013506907726 chr12 133851895 183671887 1.3722023659059888 4.643212354759904 chr13 115169878 112277861 0.9748891198790711 3.6173251217415605 chr14 107349540 127858781 1.1910510375731465 4.419815527499638 chr15 102531392 129712067 1.2650961278278559 4.60963711419818 chr16 90354753 141946423 1.5709901060766553 9.910443871858408 chr17 81195210 120257202 1.4810873941948053 5.41431387957445 chr18 78077248 101447455 1.299321602626158 5.064990326040129 chr19 59128983 77598067 1.3123524718833741 5.16550914388639 chr20 63025520 114217952 1.8122492602996374 5.816195121713207 chr21 48129895 54261698 1.1274011297967719 6.651470998760993 chr22 51304566 69085485 1.346575760917654 5.479847150596255 chrMT 16571 3546 0.21398829280067588 0.906636682385846 chrX 155270560 216713265 1.3957138107829328 4.586504931275815 chrY 59373566 5665034 0.09541340333171162 3.4597637321085286