BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818869.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 768,795 number of mapped reads = 757,625 (98.55%) number of supplementary alignments = 12,228 (1.59%) number of secondary alignments = 0 number of mapped bases = 70,110,112 bp number of sequenced bases = 70,063,976 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 133,258 duplication rate = 14.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3244 >>>>>>> ACTG content number of A's = 20,084,302 bp (28.67%) number of C's = 15,581,871 bp (22.24%) number of T's = 19,584,832 bp (27.95%) number of G's = 14,812,053 bp (21.14%) number of N's = 918 bp (0%) GC percentage = 43.38% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 421,740 number of insertions = 9,871 mapped reads with insertion percentage = 1.26% number of deletions = 23,577 mapped reads with deletion percentage = 3.04% homopolymer indels = 40.62% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.285X There is a 1.74% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% 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 6250675 0.025077871320529226 0.3671411113964076 chr2 243199373 5104758 0.020990012996456205 0.4375630351146176 chr3 198022430 4045870 0.020431372345041922 0.17735616122967934 chr4 191154276 3989373 0.020869912426128515 0.21238462513346112 chr5 180915260 3601749 0.019908486437241392 0.18100511561543975 chr6 171115067 3292426 0.01924100581978558 0.18429217625115416 chr7 159138663 5885718 0.03698484006994579 0.5016726745330369 chr8 146364022 6692826 0.045727262127300654 0.29723693799374984 chr9 141213431 2496182 0.017676661365164336 0.2436306758841875 chr10 135534747 3129785 0.023092122642173817 0.3573311310544638 chr11 135006516 2923919 0.02165761391842746 0.20144579361846138 chr12 133851895 2577211 0.01925419882923585 0.17250859127724372 chr13 115169878 1710958 0.014855950442180724 0.15129615625074905 chr14 107349540 2269301 0.021139363987959334 0.18645134212621486 chr15 102531392 1940271 0.01892367754063068 0.17144984694149992 chr16 90354753 1723833 0.01907849828331665 0.3492947509443366 chr17 81195210 1885336 0.023219793384363436 0.21186776739287905 chr18 78077248 1188726 0.01522499870897089 0.25143097394039354 chr19 59128983 1380148 0.02334131131597511 0.3372379926670951 chr20 63025520 2873740 0.04559645045372097 0.2804879694254511 chr21 48129895 832942 0.017306125434098703 0.18271534290426192 chr22 51304566 872067 0.016997843817643833 0.17313042966938252 chrMT 16571 92548 5.584937541488142 4.123888269992354 chrX 155270560 3090784 0.01990579540641832 0.18988456578672339 chrY 59373566 258966 0.0043616379720227685 0.3214862872007704