BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006441.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 7,263,973 number of mapped reads = 6,819,531 (93.88%) number of supplementary alignments = 21,479 (0.3%) number of secondary alignments = 0 number of mapped bases = 381,182,989 bp number of sequenced bases = 381,049,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 955,893 duplication rate = 12.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7448 >>>>>>> ACTG content number of A's = 108,105,126 bp (28.37%) number of C's = 78,472,275 bp (20.59%) number of T's = 111,628,126 bp (29.29%) number of G's = 82,836,019 bp (21.74%) number of N's = 8,072 bp (0%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 1,591,460 number of insertions = 24,908 mapped reads with insertion percentage = 0.36% number of deletions = 80,005 mapped reads with deletion percentage = 1.17% homopolymer indels = 43.69% >>>>>>> Coverage mean coverageData = 0.1231X std coverageData = 1.2714X There is a 5.03% of reference with a coverageData >= 1X There is a 2.73% of reference with a coverageData >= 2X There is a 1.64% of reference with a coverageData >= 3X There is a 1% of reference with a coverageData >= 4X There is a 0.62% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 30576401 0.12267331923718658 1.2506600333240827 chr2 243199373 33250691 0.13672194376915603 0.8748943031680385 chr3 198022430 26303364 0.13283022534366434 0.7414781105928681 chr4 191154276 24582768 0.12860171644813218 0.7657334139006553 chr5 180915260 23808392 0.13159968926888754 0.7362287655261008 chr6 171115067 21993484 0.12853037657987185 0.751541850805738 chr7 159138663 19162934 0.12041658286396437 0.9168375075348342 chr8 146364022 19918505 0.13608880603185392 4.458321872945678 chr9 141213431 16263015 0.11516620540152445 0.7900765837525036 chr10 135534747 18921982 0.13960982271210495 0.9890712706222528 chr11 135006516 17879063 0.13243111169537922 0.8093321224478941 chr12 133851895 17230965 0.12873157305692234 0.7291492887918104 chr13 115169878 12135760 0.10537269128651851 0.6570548932675402 chr14 107349540 11974115 0.11154323530403577 0.6954979640040918 chr15 102531392 11747580 0.1145754463179433 0.7047173238807619 chr16 90354753 11345091 0.12556164034890338 0.7788492018713788 chr17 81195210 10244144 0.12616685146820852 0.7950467552150922 chr18 78077248 10140391 0.1298763885735317 1.0182828652151896 chr19 59128983 7934173 0.13418416142892226 1.0625726547176233 chr20 63025520 8378771 0.13294251281068367 0.7820518235497917 chr21 48129895 7104774 0.14761665281006742 0.8659799052927838 chr22 51304566 4646901 0.09057480380985973 0.7015780984580292 chrMT 16571 127206 7.676422666103433 6.547915871738838 chrX 155270560 11994117 0.07724656238761553 0.5613897605721695 chrY 59373566 3518402 0.0592587280339537 0.7249942267349753