BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927029.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 = 23,063,604 number of mapped reads = 22,518,355 (97.64%) number of supplementary alignments = 641,174 (2.78%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,297,194 number of mapped paired reads (second in pair) = 11,221,161 number of mapped paired reads (both in pair) = 22,216,168 number of mapped paired reads (singletons) = 302,187 number of mapped bases = 2,071,553,659 bp number of sequenced bases = 2,069,997,185 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,709,918 duplication rate = 6.06% >>>>>>> Insert size mean insert size = 292,318.2553 std insert size = 5,287,043.5423 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 52.8502 >>>>>>> ACTG content number of A's = 586,296,754 bp (28.32%) number of C's = 413,297,582 bp (19.97%) number of T's = 595,503,935 bp (28.77%) number of G's = 474,619,102 bp (22.93%) number of N's = 279,812 bp (0.01%) GC percentage = 42.89% >>>>>>> Mismatches and indels general error rate = 0.0111 number of mismatches = 22,345,875 number of insertions = 347,806 mapped reads with insertion percentage = 1.52% number of deletions = 1,067,527 mapped reads with deletion percentage = 4.62% homopolymer indels = 51.7% >>>>>>> Coverage mean coverageData = 0.6692X std coverageData = 2.4534X There is a 30.29% of reference with a coverageData >= 1X There is a 15.44% of reference with a coverageData >= 2X There is a 8.11% of reference with a coverageData >= 3X There is a 4.61% of reference with a coverageData >= 4X There is a 2.72% of reference with a coverageData >= 5X There is a 1.66% of reference with a coverageData >= 6X There is a 1.05% of reference with a coverageData >= 7X There is a 0.67% of reference with a coverageData >= 8X There is a 0.44% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 172908561 0.6937136618006661 3.087102846130108 chr2 243199373 180461976 0.7420330643697836 4.445275178389839 chr3 198022430 139088338 0.7023867851737806 1.4523021087272594 chr4 191154276 123713213 0.6471904034205335 2.2232336497593015 chr5 180915260 123888001 0.6847846942264572 1.4277285991541067 chr6 171115067 117576431 0.6871191009731481 1.4471628133526444 chr7 159138663 107089224 0.6729302733930849 1.8566791669550604 chr8 146364022 98014394 0.6696617970774266 1.6765304733094706 chr9 141213431 91433184 0.647482207269647 2.878570268813869 chr10 135534747 101876896 0.7516662572144691 3.7723898217150333 chr11 135006516 100161582 0.7419018353158598 2.3017185665248805 chr12 133851895 94105083 0.7030537968849825 1.4717439669237558 chr13 115169878 61876514 0.5372629985767633 1.2652877426675624 chr14 107349540 62553345 0.5827071545905087 1.379869893604614 chr15 102531392 61492701 0.5997451102585245 1.3722435412279221 chr16 90354753 65969040 0.7301114530189685 3.2896188246722815 chr17 81195210 55940439 0.6889623045497388 1.8101600066356291 chr18 78077248 54886375 0.7029752764851548 3.005201428338597 chr19 59128983 36033236 0.6094005709518122 2.046959714864994 chr20 63025520 49774277 0.7897479782792748 1.703393858581291 chr21 48129895 26512554 0.5508541832472312 2.0999314314061466 chr22 51304566 25324076 0.49360277211973685 1.3636917199749694 chrMT 16571 542749 32.7529418864281 24.409982821738247 chrX 155270560 116149227 0.7480441044329331 1.6611465872227091 chrY 59373566 4182243 0.07043947806672081 3.0209817175243536