BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082424.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 = 2,997,463 number of mapped reads = 2,634,848 (87.9%) number of supplementary alignments = 23,563 (0.79%) number of secondary alignments = 0 number of mapped bases = 176,671,086 bp number of sequenced bases = 176,606,270 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,191 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7765 >>>>>>> ACTG content number of A's = 49,032,353 bp (27.76%) number of C's = 33,002,274 bp (18.69%) number of T's = 55,274,596 bp (31.3%) number of G's = 39,293,277 bp (22.25%) number of N's = 3,770 bp (0%) GC percentage = 40.94% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,508,535 number of insertions = 14,489 mapped reads with insertion percentage = 0.54% number of deletions = 40,287 mapped reads with deletion percentage = 1.51% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 0.0571X std coverageData = 0.5135X There is a 4.93% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 13878922 0.05568259747685844 0.9513222652882459 chr2 243199373 15152661 0.062305510137972274 0.6478642908354758 chr3 198022430 11914243 0.060166128655223555 0.27271804524631404 chr4 191154276 11790499 0.06168054017269276 0.29508540986055176 chr5 180915260 11081799 0.061254086581751035 0.2800615429653011 chr6 171115067 10438346 0.06100191048635127 0.35718545794792883 chr7 159138663 9844821 0.06186316269353099 0.6922147888215313 chr8 146364022 9094590 0.06213678659363433 0.8024446600251612 chr9 141213431 7452907 0.05277760725182012 0.4472151776488603 chr10 135534747 8260829 0.060949897962328435 0.4576835741934227 chr11 135006516 7962233 0.058976657097054484 0.4255981872279653 chr12 133851895 8006789 0.05981827153063466 0.28206841056845616 chr13 115169878 5768468 0.050086603373843984 0.2491978842968819 chr14 107349540 5366081 0.0499869957523805 0.2776478562089684 chr15 102531392 5023853 0.0489981936459031 0.2592978289195279 chr16 90354753 4830983 0.05346683865097833 0.3032346329890151 chr17 81195210 4495562 0.05536733016639775 0.30155449453431865 chr18 78077248 4763854 0.061014624900713715 0.8647938319128807 chr19 59128983 3293418 0.05569887782443341 0.736347608630749 chr20 63025520 3435323 0.054506856904948976 0.2719571167427582 chr21 48129895 2273276 0.04723209971681842 0.2619582929489158 chr22 51304566 1834523 0.03575749963463291 0.20861991128646412 chrMT 16571 4595 0.27729165409450246 0.6173911990207859 chrX 155270560 10258069 0.06606576932549223 0.3447908847540585 chrY 59373566 444442 0.007485519734489251 0.16222649049384474