BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472428.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 = 21,789,822
number of mapped reads = 21,621,072 (99.23%)
number of supplementary alignments = 85,108 (0.39%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 10,836,763
number of mapped paired reads (second in pair) = 10,784,309
number of mapped paired reads (both in pair) = 21,527,980
number of mapped paired reads (singletons) = 93,092
number of mapped bases = 2,120,488,527 bp
number of sequenced bases = 2,120,247,800 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 14,651,119
duplication rate = 48.56%
>>>>>>> Insert size
mean insert size = 16,568.1293
std insert size = 1,296,536.9718
median insert size = 203
>>>>>>> Mapping quality
mean mapping quality = 54.6655
>>>>>>> ACTG content
number of A's = 580,153,190 bp (27.36%)
number of C's = 480,267,715 bp (22.65%)
number of T's = 583,130,520 bp (27.5%)
number of G's = 476,435,274 bp (22.47%)
number of N's = 261,101 bp (0.01%)
GC percentage = 45.12%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 10,585,012
number of insertions = 139,866
mapped reads with insertion percentage = 0.64%
number of deletions = 106,338
mapped reads with deletion percentage = 0.48%
homopolymer indels = 46.37%
>>>>>>> Coverage
mean coverageData = 0.685X
std coverageData = 24.0551X
There is a 5.61% of reference with a coverageData >= 1X
There is a 2.56% of reference with a coverageData >= 2X
There is a 1.06% of reference with a coverageData >= 3X
There is a 0.75% of reference with a coverageData >= 4X
There is a 0.53% of reference with a coverageData >= 5X
There is a 0.46% of reference with a coverageData >= 6X
There is a 0.41% of reference with a coverageData >= 7X
There is a 0.39% of reference with a coverageData >= 8X
There is a 0.37% of reference with a coverageData >= 9X
There is a 0.35% of reference with a coverageData >= 10X
There is a 0.34% of reference with a coverageData >= 11X
There is a 0.33% of reference with a coverageData >= 12X
There is a 0.32% of reference with a coverageData >= 13X
There is a 0.31% of reference with a coverageData >= 14X
There is a 0.3% of reference with a coverageData >= 15X
There is a 0.3% of reference with a coverageData >= 16X
There is a 0.29% of reference with a coverageData >= 17X
There is a 0.28% of reference with a coverageData >= 18X
There is a 0.28% of reference with a coverageData >= 19X
There is a 0.27% of reference with a coverageData >= 20X
There is a 0.27% of reference with a coverageData >= 21X
There is a 0.26% of reference with a coverageData >= 22X
There is a 0.26% of reference with a coverageData >= 23X
There is a 0.25% 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 0.23% 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 0.21% 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 0.2% 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 0.19% of reference with a coverageData >= 47X
There is a 0.19% 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 177685905 0.7128804906768919 21.62053810201715
chr2 243199373 194871799 0.8012841340672371 27.614493018409274
chr3 198022430 153137769 0.7733354701283082 20.301645785538856
chr4 191154276 58350114 0.30525141901612496 12.380001705414768
chr5 180915260 116087703 0.6416689393697359 30.852778127360928
chr6 171115067 174410190 1.0192567671437138 26.041295566012302
chr7 159138663 165742980 1.0415003926481399 34.033628833377605
chr8 146364022 209969693 1.4345717624512941 45.59443282762567
chr9 141213431 79662897 0.5641311625662576 18.051548320432186
chr10 135534747 38113082 0.2812052469467479 10.595637779643047
chr11 135006516 73641572 0.5454667980618061 21.565852511548663
chr12 133851895 74459695 0.556284205016298 13.022119401596683
chr13 115169878 81408490 0.7068557457358772 31.26041570569999
chr14 107349540 42995280 0.40051666732805746 14.002804649984366
chr15 102531392 38639783 0.3768580748420932 15.033883284407178
chr16 90354753 114954883 1.2722616042124535 33.21602695550246
chr17 81195210 67062429 0.8259407051228761 20.107301632640613
chr18 78077248 14257359 0.18260580854489133 8.247629625783794
chr19 59128983 25463257 0.4306391841713225 9.679302901047924
chr20 63025520 61104056 0.9695129211151292 28.415647001298346
chr21 48129895 13109417 0.27237576562342386 14.558428610709031
chr22 51304566 25842043 0.5036986961355447 27.831186808599
chrMT 16571 11907 0.7185444451149599 1.1975094166015252
chrX 155270560 118931169 0.7659608428023961 18.563350728541767
chrY 59373566 575055 0.009685370759101785 1.2665386308255777