BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006144.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 20,273,330 number of mapped reads = 17,774,660 (87.68%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,039,909 number of mapped paired reads (second in pair) = 8,734,751 number of mapped paired reads (both in pair) = 16,234,374 number of mapped paired reads (singletons) = 1,540,286 number of mapped bases = 687,003,904 bp number of sequenced bases = 686,928,949 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,658,446 duplication rate = 8.25% >>>>>>> Insert size mean insert size = 61,621.0976 std insert size = 2,406,839.1173 median insert size = 110 >>>>>>> Mapping quality mean mapping quality = 47.5561 >>>>>>> ACTG content number of A's = 188,370,243 bp (27.42%) number of C's = 148,401,443 bp (21.6%) number of T's = 194,195,599 bp (28.27%) number of G's = 155,934,909 bp (22.7%) number of N's = 26,755 bp (0%) GC percentage = 44.3% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 3,001,430 number of insertions = 20,981 mapped reads with insertion percentage = 0.12% number of deletions = 59,113 mapped reads with deletion percentage = 0.33% homopolymer indels = 47.02% >>>>>>> Coverage mean coverageData = 0.2219X std coverageData = 1.0377X There is a 10.56% of reference with a coverageData >= 1X There is a 5.33% of reference with a coverageData >= 2X There is a 2.74% of reference with a coverageData >= 3X There is a 1.45% of reference with a coverageData >= 4X There is a 0.8% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 56968842 0.22856048170086604 1.1293931927496372 chr2 243199373 59543435 0.24483383433722916 1.1499350083733508 chr3 198022430 47768597 0.241228213389766 0.8689232255560397 chr4 191154276 43105571 0.22550147400312406 0.888634696868199 chr5 180915260 42415004 0.23444680122616524 0.8599515487118419 chr6 171115067 40190539 0.23487434335633342 0.9780266164067593 chr7 159138663 38068036 0.23921299376506638 1.538650809815681 chr8 146364022 34965079 0.2388912146729611 1.1476121826456969 chr9 141213431 29075418 0.20589697307191693 0.9746667086503111 chr10 135534747 33079100 0.24406361270589896 0.9440940392665121 chr11 135006516 31721884 0.23496557751331054 1.5091611466825106 chr12 133851895 32581320 0.24341321428434018 0.8886268718743641 chr13 115169878 21945190 0.19054626418897483 0.7737967352082405 chr14 107349540 21471571 0.20001549144970718 0.8327041913112219 chr15 102531392 21167674 0.20645066439749496 0.8233242652326174 chr16 90354753 21320173 0.23596072472247254 0.9912100343221697 chr17 81195210 19634576 0.24181938811415107 1.007845820676595 chr18 78077248 17865421 0.22881724775955217 1.3759837900290894 chr19 59128983 14372359 0.24306792153012338 1.2370229460697235 chr20 63025520 16162713 0.2564471185640356 0.9290537967871803 chr21 48129895 9404913 0.1954068879643307 0.914332884391571 chr22 51304566 8915032 0.17376683393053163 0.8476230112865522 chrMT 16571 33756 2.0370526823969586 3.3500758776904482 chrX 155270560 20677220 0.13316896648018786 0.7190721233873146 chrY 59373566 4550481 0.07664153101398694 0.5863270925268936