BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068156.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,451,888 number of mapped reads = 4,199,419 (94.33%) number of supplementary alignments = 43,083 (0.97%) number of secondary alignments = 0 number of mapped bases = 268,036,399 bp number of sequenced bases = 267,921,641 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 542,374 duplication rate = 10.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4073 >>>>>>> ACTG content number of A's = 70,939,901 bp (26.48%) number of C's = 48,073,386 bp (17.94%) number of T's = 87,283,879 bp (32.58%) number of G's = 61,594,110 bp (22.99%) number of N's = 30,365 bp (0.01%) GC percentage = 40.93% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,505,010 number of insertions = 16,716 mapped reads with insertion percentage = 0.4% number of deletions = 66,549 mapped reads with deletion percentage = 1.57% homopolymer indels = 43.88% >>>>>>> Coverage mean coverageData = 0.0866X std coverageData = 0.9292X There is a 6.18% of reference with a coverageData >= 1X There is a 1.6% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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% 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 29084812 0.11668902522012171 2.3304962683857533 chr2 243199373 25926768 0.10660705116209325 1.3920082074228073 chr3 198022430 18170732 0.09176097879416993 0.4013882059945437 chr4 191154276 8190975 0.04285007466953028 0.30036063104652755 chr5 180915260 14824402 0.08194113641933798 0.3837020055450537 chr6 171115067 19811592 0.11577935448548199 0.599546964380664 chr7 159138663 23903723 0.15020688592815437 0.9320927162894532 chr8 146364022 11443005 0.07818181574704199 0.8307887649606228 chr9 141213431 7142029 0.05057613110469641 0.4869302002638909 chr10 135534747 11445843 0.08444951020567441 0.48543696231340244 chr11 135006516 13479877 0.09984612150127628 0.5225731916088631 chr12 133851895 7570172 0.05655633041280439 0.33301245308069927 chr13 115169878 7406963 0.06431337020258023 0.3837482319347436 chr14 107349540 5967750 0.05559176126884195 0.3518206856472196 chr15 102531392 4665214 0.0455003478349343 0.3193094115075775 chr16 90354753 3861812 0.042740551789234596 0.3147379910567253 chr17 81195210 7802682 0.09609781168125558 0.438416614772514 chr18 78077248 7444736 0.09535090171210953 0.966719102256282 chr19 59128983 6941361 0.1173935462411048 1.476179425281825 chr20 63025520 3470094 0.055058554058736844 0.33000671036424994 chr21 48129895 5155200 0.10711014432921576 0.4456666499977573 chr22 51304566 1727350 0.033668543263771104 0.23418119252412145 chrMT 16571 279098 16.84255627300706 10.546078600136912 chrX 155270560 21574716 0.13894917362312598 0.5757926766961817 chrY 59373566 745493 0.01255597482556463 0.33414039984887867