BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472407.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,647,306 number of mapped reads = 18,512,999 (99.28%) number of supplementary alignments = 74,213 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,283,215 number of mapped paired reads (second in pair) = 9,229,784 number of mapped paired reads (both in pair) = 18,428,810 number of mapped paired reads (singletons) = 84,189 number of mapped bases = 1,818,379,486 bp number of sequenced bases = 1,818,173,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,943,797 duplication rate = 47.7% >>>>>>> Insert size mean insert size = 17,194.0772 std insert size = 1,317,561.8111 median insert size = 216 >>>>>>> Mapping quality mean mapping quality = 55.2415 >>>>>>> ACTG content number of A's = 488,691,107 bp (26.88%) number of C's = 421,877,079 bp (23.2%) number of T's = 489,616,784 bp (26.93%) number of G's = 417,763,619 bp (22.98%) number of N's = 224,731 bp (0.01%) GC percentage = 46.18% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 9,522,030 number of insertions = 105,886 mapped reads with insertion percentage = 0.57% number of deletions = 84,766 mapped reads with deletion percentage = 0.45% homopolymer indels = 46.47% >>>>>>> Coverage mean coverageData = 0.5874X std coverageData = 19.1604X There is a 4.96% of reference with a coverageData >= 1X There is a 2.18% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.51% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.35% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.3% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.28% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.27% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.25% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.24% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.2% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.19% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 221326359 0.887967131684699 22.585504098600207 chr2 243199373 127307880 0.5234712508901082 16.889678095900454 chr3 198022430 171854151 0.8678519448529138 21.54303400422809 chr4 191154276 61395746 0.32118426689026824 15.742475223451809 chr5 180915260 75881707 0.41943231875520065 14.733140721085737 chr6 171115067 129485654 0.7567168471494097 19.05221919729643 chr7 159138663 98293211 0.6176576398659325 18.778198076037647 chr8 146364022 123566001 0.844237534002721 25.100223917549965 chr9 141213431 66686986 0.47224251636517495 14.807098825514672 chr10 135534747 48080125 0.35474390194567595 12.66088048438355 chr11 135006516 98168269 0.7271372664709013 27.37719405025988 chr12 133851895 91344179 0.6824272379558018 23.918603243875395 chr13 115169878 43564163 0.3782600429601914 13.94781127963886 chr14 107349540 43602257 0.40617087879463665 12.0041650125166 chr15 102531392 36562128 0.35659447596302996 11.119766470126725 chr16 90354753 102665562 1.136249711180108 37.04859575913924 chr17 81195210 59921031 0.7379872655049479 18.213691029909782 chr18 78077248 28142149 0.36043981724355856 11.58038701153633 chr19 59128983 51111705 0.8644103518573962 28.60549210278855 chr20 63025520 43672777 0.692937987659602 19.2654484704932 chr21 48129895 7207289 0.14974661798036334 7.107861377838859 chr22 51304566 23962126 0.4670564019584534 12.309580467593115 chrMT 16571 3421 0.20644499426709312 0.5646948259820576 chrX 155270560 62001479 0.39931252260570194 12.991339122654658 chrY 59373566 2573131 0.04333798983877775 1.82841649485676