BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085124.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 = 2,114,984 number of mapped reads = 1,890,603 (89.39%) number of supplementary alignments = 15,604 (0.74%) number of secondary alignments = 0 number of mapped bases = 126,214,398 bp number of sequenced bases = 126,169,788 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,988 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7858 >>>>>>> ACTG content number of A's = 35,197,684 bp (27.9%) number of C's = 23,224,573 bp (18.41%) number of T's = 39,864,085 bp (31.6%) number of G's = 27,863,745 bp (22.08%) number of N's = 19,701 bp (0.02%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,124,447 number of insertions = 9,943 mapped reads with insertion percentage = 0.52% number of deletions = 27,777 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.5% >>>>>>> Coverage mean coverageData = 0.0408X std coverageData = 0.3671X There is a 3.63% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 10015496 0.04018243148128405 0.6642891979631778 chr2 243199373 10933013 0.04495493909024181 0.43918347466223284 chr3 198022430 8564812 0.04325172658471063 0.22638065309105848 chr4 191154276 8526201 0.044603768110319436 0.23606376088401332 chr5 180915260 7817074 0.04320848335292446 0.22816582868461635 chr6 171115067 7476751 0.043694287891083254 0.2749056401227547 chr7 159138663 7106171 0.044653956908007955 0.4999963668874704 chr8 146364022 6530983 0.04462150541340002 0.52772146891612 chr9 141213431 5304137 0.03756113680149872 0.3406447353321315 chr10 135534747 5895378 0.04349717050786984 0.3377598477378095 chr11 135006516 5631442 0.041712371868036356 0.2939531173693633 chr12 133851895 5727001 0.04278610325240446 0.22975676306975606 chr13 115169878 4109926 0.03568577193422051 0.20869525332837577 chr14 107349540 3900037 0.03633026280317549 0.22500870335277884 chr15 102531392 3508244 0.034216291533426174 0.20675224112162172 chr16 90354753 3371506 0.03731409680241171 0.2329066438007208 chr17 81195210 3112474 0.03833322187355633 0.23628928344505112 chr18 78077248 3405813 0.043621068713897294 0.5981177125645523 chr19 59128983 2281559 0.03858613634535199 0.5060835736508585 chr20 63025520 2428965 0.038539388488980336 0.21896847471473993 chr21 48129895 1647453 0.03422930800077582 0.21216496682587696 chr22 51304566 1272496 0.02480278266070899 0.1693560849343989 chrMT 16571 4821 0.2909299378432201 0.578555600730682 chrX 155270560 7333780 0.047232263476089734 0.2666033428446341 chrY 59373566 308865 0.005202062480127941 0.11336343768101759