BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089526.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 23,892,841 number of mapped reads = 19,221,640 (80.45%) number of supplementary alignments = 753 (0%) number of secondary alignments = 0 number of mapped bases = 890,766,104 bp number of sequenced bases = 890,594,096 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,071,005 duplication rate = 8.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5897 >>>>>>> ACTG content number of A's = 269,764,702 bp (30.29%) number of C's = 188,059,794 bp (21.12%) number of T's = 239,098,662 bp (26.85%) number of G's = 193,587,013 bp (21.74%) number of N's = 83,925 bp (0.01%) GC percentage = 42.85% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 3,764,652 number of insertions = 37,889 mapped reads with insertion percentage = 0.2% number of deletions = 115,110 mapped reads with deletion percentage = 0.6% homopolymer indels = 42.57% >>>>>>> Coverage mean coverageData = 0.2877X std coverageData = 1.3452X There is a 14.94% of reference with a coverageData >= 1X There is a 6.18% of reference with a coverageData >= 2X There is a 3.01% of reference with a coverageData >= 3X There is a 1.62% of reference with a coverageData >= 4X There is a 0.94% of reference with a coverageData >= 5X There is a 0.57% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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% 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 73788825 0.29604269270807554 1.8621614010393124 chr2 243199373 85138090 0.3500752857615303 1.7027818138698378 chr3 198022430 47892936 0.24185611700654314 0.8468150387253562 chr4 191154276 26465917 0.1384531779974412 0.7523175400309582 chr5 180915260 54285014 0.30005768446509157 0.9702596762867123 chr6 171115067 42134946 0.2462374981859429 0.926431027706198 chr7 159138663 54336284 0.341439867444406 1.9781868040259032 chr8 146364022 47263564 0.3229179094299554 1.4908316586213717 chr9 141213431 42526354 0.3011494990161382 1.375129090694025 chr10 135534747 45859903 0.3383627004520103 1.403572630586594 chr11 135006516 52762990 0.39081809947602825 1.6151735857902292 chr12 133851895 37156625 0.2775950613175854 0.9635289431081268 chr13 115169878 26403895 0.22926042345898812 0.8381413447730041 chr14 107349540 30612091 0.28516275896477994 1.1231604353415146 chr15 102531392 28929112 0.28214882716114886 0.9560511591108379 chr16 90354753 25679171 0.2842038758049618 1.0565285115876566 chr17 81195210 25170788 0.3100033610357064 1.1373753582211017 chr18 78077248 25596827 0.32783976965991424 2.0881793184689554 chr19 59128983 18379120 0.3108309845275032 1.784722079886065 chr20 63025520 20128764 0.31937481832756 1.067344857206126 chr21 48129895 9837323 0.2043911169970348 1.0165399471324068 chr22 51304566 10777436 0.21006777447449804 0.8267505486415323 chrMT 16571 86578 5.224669603524229 5.622319736263995 chrX 155270560 56974784 0.36693874228314755 1.3143893498451875 chrY 59373566 2578767 0.043432914236614995 0.6067118050153464