BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818944.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,211,066 number of mapped reads = 1,193,554 (98.55%) number of supplementary alignments = 14,645 (1.21%) number of secondary alignments = 0 number of mapped bases = 110,660,028 bp number of sequenced bases = 110,596,192 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 427,874 duplication rate = 29.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.9739 >>>>>>> ACTG content number of A's = 30,559,197 bp (27.63%) number of C's = 23,739,407 bp (21.46%) number of T's = 31,734,058 bp (28.69%) number of G's = 24,558,977 bp (22.21%) number of N's = 4,553 bp (0%) GC percentage = 43.67% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 702,803 number of insertions = 13,532 mapped reads with insertion percentage = 1.1% number of deletions = 34,496 mapped reads with deletion percentage = 2.83% homopolymer indels = 42% >>>>>>> Coverage mean coverageData = 0.0357X std coverageData = 0.447X There is a 1.99% of reference with a coverageData >= 1X There is a 0.76% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 16271076 0.06527998178989491 0.7450564941179243 chr2 243199373 9324310 0.03834018930632687 0.6516486603761259 chr3 198022430 7013978 0.035420118821893054 0.30879827315724084 chr4 191154276 6721886 0.03516471690123218 0.32485773927943834 chr5 180915260 5495561 0.03037643701255494 0.2996680713200819 chr6 171115067 5788823 0.03383000165613704 0.3225906401754543 chr7 159138663 5450011 0.03424693218642914 0.3600188407999982 chr8 146364022 7178099 0.04904278320528798 0.3959067940379083 chr9 141213431 3843860 0.027220215334899694 0.42682717657063235 chr10 135534747 5462915 0.04030637988352906 0.5713470318975258 chr11 135006516 4119075 0.03051019404130094 0.3139072583448613 chr12 133851895 4769693 0.035634108878324064 0.3127709225799843 chr13 115169878 1722878 0.014959449726950305 0.19440784203360578 chr14 107349540 2508427 0.023366909629980715 0.2826563964665289 chr15 102531392 3076362 0.030004098647173346 0.28530913783763745 chr16 90354753 3419520 0.03784549109441979 0.496530713851581 chr17 81195210 2395964 0.029508686534587446 0.3182322919328174 chr18 78077248 2724418 0.034893878431780795 0.619717585173703 chr19 59128983 1696224 0.028686845501807463 0.6961027682566787 chr20 63025520 2339730 0.037123533451211506 0.33315224764534246 chr21 48129895 1458613 0.030305759029808813 0.3249060686626292 chr22 51304566 1350397 0.026321185525670365 0.28706949674235605 chrMT 16571 180640 10.900971576851125 9.846909136212588 chrX 155270560 6021842 0.038782896126606355 0.38878165800389575 chrY 59373566 325726 0.005486044075573969 0.4040952221989789