BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085035.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,354,159 number of mapped reads = 2,111,414 (89.69%) number of supplementary alignments = 12,650 (0.54%) number of secondary alignments = 0 number of mapped bases = 142,537,190 bp number of sequenced bases = 142,484,806 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,735 duplication rate = 3.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0851 >>>>>>> ACTG content number of A's = 38,972,554 bp (27.35%) number of C's = 27,480,826 bp (19.29%) number of T's = 43,877,221 bp (30.79%) number of G's = 32,139,302 bp (22.56%) number of N's = 14,903 bp (0.01%) GC percentage = 41.84% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,263,887 number of insertions = 9,537 mapped reads with insertion percentage = 0.45% number of deletions = 29,866 mapped reads with deletion percentage = 1.4% homopolymer indels = 48.26% >>>>>>> Coverage mean coverageData = 0.046X std coverageData = 0.3299X There is a 3.82% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.11% 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 12491228 0.05011513291274809 0.4810903720573523 chr2 243199373 14878310 0.06117741923619186 0.40885703811224633 chr3 198022430 8675099 0.04380866854325543 0.24479929498430555 chr4 191154276 7596966 0.03974258990680386 0.23976010275219617 chr5 180915260 7331526 0.04052464120494866 0.23388196058852587 chr6 171115067 8893982 0.051976615244524314 0.3191692685419088 chr7 159138663 11842711 0.07441755998666395 0.4468903912902597 chr8 146364022 8823986 0.06028794425996301 0.46954063546527175 chr9 141213431 4582705 0.03245233096843317 0.2689775062618865 chr10 135534747 10281168 0.07585632634854883 0.4223317550031879 chr11 135006516 6122830 0.045352107301250555 0.34808087319304204 chr12 133851895 6177741 0.046153556511097586 0.2533489762391127 chr13 115169878 2714350 0.023568228491133766 0.1770694155019235 chr14 107349540 4335110 0.04038312600128515 0.2381961673708838 chr15 102531392 2369870 0.023113604075520596 0.18036283653236115 chr16 90354753 4316906 0.047777298444941795 0.26188038813910186 chr17 81195210 2538668 0.03126622863590106 0.23918326687078675 chr18 78077248 3796264 0.048621898148869185 0.4282941077809558 chr19 59128983 2388684 0.04039785362112519 0.354234851336975 chr20 63025520 3323038 0.05272527699890457 0.2734764920621068 chr21 48129895 1645081 0.034180024701903046 0.22476674455595444 chr22 51304566 881086 0.0171736371378719 0.15003401710504832 chrMT 16571 7137 0.43069217307344154 0.745068527264774 chrX 155270560 6225658 0.040095546766882276 0.24822011716919984 chrY 59373566 297086 0.005003674530850985 0.11210029119614019