BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006088.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 = 6,989,502 number of mapped reads = 6,150,889 (88%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,111,134 number of mapped paired reads (second in pair) = 3,039,755 number of mapped paired reads (both in pair) = 5,633,848 number of mapped paired reads (singletons) = 517,041 number of mapped bases = 237,487,477 bp number of sequenced bases = 237,462,025 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 315,737 duplication rate = 4.66% >>>>>>> Insert size mean insert size = 63,552.5553 std insert size = 2,462,895.9383 median insert size = 103 >>>>>>> Mapping quality mean mapping quality = 47.0382 >>>>>>> ACTG content number of A's = 62,739,292 bp (26.42%) number of C's = 53,126,808 bp (22.37%) number of T's = 65,001,391 bp (27.37%) number of G's = 56,584,574 bp (23.83%) number of N's = 9,960 bp (0%) GC percentage = 46.2% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 1,161,196 number of insertions = 7,460 mapped reads with insertion percentage = 0.12% number of deletions = 19,899 mapped reads with deletion percentage = 0.32% homopolymer indels = 43.81% >>>>>>> Coverage mean coverageData = 0.0767X std coverageData = 0.4273X There is a 5.08% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 20337027 0.08159268337389619 0.45705118992972665 chr2 243199373 20269467 0.08334506273583198 0.46351218184749127 chr3 198022430 16388616 0.08276141243191491 0.40517084873124143 chr4 191154276 14325336 0.07494122705369144 0.3983556636401707 chr5 180915260 14047138 0.07764484875405203 0.39153062157581814 chr6 171115067 13313772 0.07780595965871316 0.4277898117973335 chr7 159138663 12534614 0.07876535949029558 0.48110434600598917 chr8 146364022 11758981 0.08034065229500184 0.4543811329236455 chr9 141213431 10444641 0.07396350988738458 0.40649593046282356 chr10 135534747 11430354 0.08433522954818369 0.4235087359514325 chr11 135006516 11597359 0.0859022167493012 0.5540978359196704 chr12 133851895 10690296 0.07986660181389288 0.40035282462151617 chr13 115169878 7111001 0.06174358368253199 0.3532951993697168 chr14 107349540 7224140 0.06729549097276057 0.37522205009953724 chr15 102531392 7512867 0.07327382232360602 0.3892084573586028 chr16 90354753 8327360 0.09216294354764049 0.48059162160141605 chr17 81195210 7371843 0.0907915996522455 0.45800398187505925 chr18 78077248 6221047 0.07967810289624962 0.4584666372371479 chr19 59128983 5348817 0.09046015555518687 0.48873946537083174 chr20 63025520 6006494 0.09530256949883159 0.4494097706823386 chr21 48129895 3167988 0.06582162707813927 0.40692081005058217 chr22 51304566 3417720 0.0666162929825778 0.40441473160394975 chrMT 16571 4658 0.28109347655542816 0.7782522590614327 chrX 155270560 7172429 0.04619310318710772 0.30579303234765126 chrY 59373566 1463512 0.024649218475440736 0.2518637066878467