BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081911.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 = 2,743,078 number of mapped reads = 2,550,428 (92.98%) number of supplementary alignments = 18,516 (0.68%) number of secondary alignments = 0 number of mapped bases = 174,579,389 bp number of sequenced bases = 174,513,032 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,395 duplication rate = 2.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9405 >>>>>>> ACTG content number of A's = 49,440,026 bp (28.33%) number of C's = 32,767,649 bp (18.78%) number of T's = 54,753,923 bp (31.38%) number of G's = 37,549,301 bp (21.52%) number of N's = 2,133 bp (0%) GC percentage = 40.29% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,491,397 number of insertions = 13,768 mapped reads with insertion percentage = 0.53% number of deletions = 40,133 mapped reads with deletion percentage = 1.56% homopolymer indels = 48.04% >>>>>>> Coverage mean coverageData = 0.0564X std coverageData = 0.426X There is a 4.78% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.1% 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 13654079 0.05478052148965358 0.7260903715585838 chr2 243199373 15156820 0.06232261133337708 0.5041100204864396 chr3 198022430 12010666 0.0606530583429362 0.279650365947716 chr4 191154276 11732256 0.06137584910734615 0.3066432471551616 chr5 180915260 11064607 0.061159058666471804 0.2819110138471967 chr6 171115067 10215540 0.059699827601972656 0.3273306328281343 chr7 159138663 9472285 0.05952221051398427 0.5476357088667623 chr8 146364022 9042159 0.06177856331387231 0.585616857226317 chr9 141213431 7365904 0.052161497301202175 0.4027005150108681 chr10 135534747 8460700 0.062424582531592436 0.4368620273362778 chr11 135006516 7886059 0.05841243247844423 0.3662872365408734 chr12 133851895 7850164 0.05864813494048777 0.2789194181859651 chr13 115169878 5944715 0.051616925390856105 0.2583194320749501 chr14 107349540 5194400 0.048387724809999186 0.26346555415850575 chr15 102531392 4801372 0.04682831185984484 0.24750583733878603 chr16 90354753 4647634 0.05143762608703053 0.2990219248705504 chr17 81195210 4338812 0.05343679756478245 0.294539615783367 chr18 78077248 4653028 0.05959518450240459 0.7464717882798897 chr19 59128983 3055946 0.0516827086303852 0.5520374888095418 chr20 63025520 3410587 0.05411438096821732 0.2740945246009419 chr21 48129895 2261188 0.04698094604195584 0.2699457194264774 chr22 51304566 1760622 0.03431706253981371 0.20862669275366005 chrMT 16571 6813 0.411139943274395 0.6605208876336217 chrX 155270560 10156170 0.06540950196869258 0.3280084412998475 chrY 59373566 436863 0.007357870335765246 0.16254671933680986