BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926969.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 28,317,738 number of mapped reads = 27,844,815 (98.33%) number of supplementary alignments = 553,903 (1.96%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,983,306 number of mapped paired reads (second in pair) = 13,861,509 number of mapped paired reads (both in pair) = 27,583,476 number of mapped paired reads (singletons) = 261,339 number of mapped bases = 2,656,993,753 bp number of sequenced bases = 2,654,987,954 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,216,759 duplication rate = 6.11% >>>>>>> Insert size mean insert size = 211,397.0159 std insert size = 4,609,838.3772 median insert size = 179 >>>>>>> Mapping quality mean mapping quality = 52.1423 >>>>>>> ACTG content number of A's = 741,482,628 bp (27.93%) number of C's = 557,092,554 bp (20.98%) number of T's = 749,046,722 bp (28.21%) number of G's = 607,126,460 bp (22.87%) number of N's = 239,590 bp (0.01%) GC percentage = 43.85% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 24,893,509 number of insertions = 431,716 mapped reads with insertion percentage = 1.52% number of deletions = 1,388,938 mapped reads with deletion percentage = 4.86% homopolymer indels = 52.57% >>>>>>> Coverage mean coverageData = 0.8583X std coverageData = 3.8969X There is a 27.49% of reference with a coverageData >= 1X There is a 16.92% of reference with a coverageData >= 2X There is a 10.81% of reference with a coverageData >= 3X There is a 7.35% of reference with a coverageData >= 4X There is a 5.16% of reference with a coverageData >= 5X There is a 3.73% of reference with a coverageData >= 6X There is a 2.75% of reference with a coverageData >= 7X There is a 2.06% of reference with a coverageData >= 8X There is a 1.58% of reference with a coverageData >= 9X There is a 1.22% of reference with a coverageData >= 10X There is a 0.95% of reference with a coverageData >= 11X There is a 0.76% of reference with a coverageData >= 12X There is a 0.6% of reference with a coverageData >= 13X There is a 0.49% of reference with a coverageData >= 14X There is a 0.4% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.19% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.13% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.1% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% 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 0.02% of reference with a coverageData >= 34X There is a 0.02% 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 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 290155155 1.1641100585261932 4.117226129323841 chr2 243199373 207452855 0.8530155832268531 4.146053297943532 chr3 198022430 226501966 1.1438197480962131 2.4585334052410084 chr4 191154276 178769998 0.9352131782811911 2.909227919565165 chr5 180915260 75824816 0.41911785661419604 1.4576061458806853 chr6 171115067 75498580 0.44121526715119713 1.9376681066491357 chr7 159138663 96803579 0.6082970484677253 2.890170331970822 chr8 146364022 162028423 1.107023575780119 2.8168863564288733 chr9 141213431 149012835 1.055231318613029 5.198303017610114 chr10 135534747 67098906 0.49506792527528015 4.381774449771575 chr11 135006516 64167471 0.47529165925591327 2.085380589417498 chr12 133851895 120171176 0.8977921156812909 2.430895188246217 chr13 115169878 59548172 0.5170464103469833 1.6815714399788648 chr14 107349540 70561773 0.6573085734694345 1.9667827224511614 chr15 102531392 81817150 0.7979717080208957 2.230117668061154 chr16 90354753 136697476 1.5128974565400006 6.391241411573632 chr17 81195210 41740055 0.5140704112964299 3.1564318375037836 chr18 78077248 67914024 0.8698311702789524 5.3564676973592755 chr19 59128983 68465819 1.1579062504761837 3.350796607138211 chr20 63025520 79745132 1.2652832059140489 2.9757273708524052 chr21 48129895 46710169 0.9705022003476218 3.760131920122967 chr22 51304566 77052900 1.5018721725469815 3.4302535923868662 chrMT 16571 11736269 708.2414458994629 485.2517804018188 chrX 155270560 195427433 1.258625157273858 2.7237415870415522 chrY 59373566 6091621 0.10259820001379065 2.2824406085128746