BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505984.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 8,094,789 number of mapped reads = 5,659,309 (69.91%) number of supplementary alignments = 322 (0%) number of secondary alignments = 0 number of mapped bases = 262,178,110 bp number of sequenced bases = 262,126,720 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 447,560 duplication rate = 6.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.356 >>>>>>> ACTG content number of A's = 78,161,472 bp (29.82%) number of C's = 52,134,232 bp (19.89%) number of T's = 78,348,739 bp (29.89%) number of G's = 53,481,094 bp (20.4%) number of N's = 1,183 bp (0%) GC percentage = 40.29% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,311,591 number of insertions = 13,218 mapped reads with insertion percentage = 0.23% number of deletions = 37,608 mapped reads with deletion percentage = 0.66% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 0.0847X std coverageData = 0.6849X There is a 6.34% of reference with a coverageData >= 1X There is a 1.42% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 21179325 0.08497200494437283 1.223202089333966 chr2 243199373 22363191 0.09195414743112845 0.5692823235444153 chr3 198022430 17537462 0.08856300773604284 0.38224646082314523 chr4 191154276 17649406 0.09233068895618113 0.39731887294747054 chr5 180915260 16305433 0.09012746077915153 0.38944489485886064 chr6 171115067 15650398 0.09146125045785711 0.4753192119074244 chr7 159138663 14947495 0.09392748888433228 1.0432403522516487 chr8 146364022 13939194 0.09523647826512993 1.180547337388201 chr9 141213431 10540978 0.07464571836654829 0.5132839033420277 chr10 135534747 12122012 0.08943840799732337 0.6995255272609427 chr11 135006516 11527170 0.08538232332430533 0.6078447078827728 chr12 133851895 11549630 0.08628663792918284 0.4005268266945859 chr13 115169878 8673187 0.07530777274939894 0.3462305427233476 chr14 107349540 8143050 0.07585547176075463 0.7454294866097466 chr15 102531392 7370786 0.07188809062496684 0.33934489888151 chr16 90354753 6862763 0.07595353616870604 0.39439297573935683 chr17 81195210 6334075 0.0780104516017632 0.4220032649350417 chr18 78077248 7279760 0.09323791740200679 1.1404289231442954 chr19 59128983 4694820 0.07939964061279389 0.9060402478350685 chr20 63025520 5126740 0.08134387467172029 0.37469525342389587 chr21 48129895 3297054 0.06850324522835548 0.3592275460228528 chr22 51304566 2774792 0.05408469881608588 0.2918333956680149 chrMT 16571 56017 3.380423631645646 3.0549496682559814 chrX 155270560 15527213 0.10000101113823509 0.48697944698640416 chrY 59373566 726159 0.012230341697852542 0.18635581936982593