BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3084764.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,940,828
number of mapped reads = 1,781,096 (91.77%)
number of supplementary alignments = 14,048 (0.72%)
number of secondary alignments = 0
number of mapped bases = 122,056,381 bp
number of sequenced bases = 122,002,637 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 66,228
duplication rate = 2.83%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.4764
>>>>>>> ACTG content
number of A's = 34,727,347 bp (28.46%)
number of C's = 22,690,877 bp (18.6%)
number of T's = 38,356,908 bp (31.44%)
number of G's = 26,178,159 bp (21.46%)
number of N's = 49,346 bp (0.04%)
GC percentage = 40.06%
>>>>>>> Mismatches and indels
general error rate = 0.009
number of mismatches = 1,081,212
number of insertions = 10,185
mapped reads with insertion percentage = 0.57%
number of deletions = 32,736
mapped reads with deletion percentage = 1.82%
homopolymer indels = 47.62%
>>>>>>> Coverage
mean coverageData = 0.0394X
std coverageData = 0.3456X
There is a 3.44% of reference with a coverageData >= 1X
There is a 0.37% of reference with a coverageData >= 2X
There is a 0.05% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% 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 9916030 0.03978337129198166 0.5499337343608723
chr2 243199373 10389161 0.042718699772305746 0.39709079978378997
chr3 198022430 8105259 0.04093101473403796 0.2246561912330599
chr4 191154276 8003063 0.04186703623621791 0.24537895467580392
chr5 180915260 7857105 0.043429752691950915 0.23217709885403487
chr6 171115067 6819128 0.039851125441805774 0.26174483556125827
chr7 159138663 6833971 0.042943498903217504 0.4597059575356579
chr8 146364022 6643361 0.045389303390419265 0.4330362433489513
chr9 141213431 4715469 0.0333924964970223 0.3381679536078101
chr10 135534747 6119604 0.045151550694228985 0.35545010605121796
chr11 135006516 5383542 0.03987616419936353 0.3080737475291843
chr12 133851895 5632682 0.042081451293610746 0.23072328988949983
chr13 115169878 4111837 0.035702364814522075 0.2092680016032067
chr14 107349540 3585643 0.03340156837188124 0.2234340099323982
chr15 102531392 3363896 0.03280844953319272 0.20389001704487456
chr16 90354753 3167827 0.03505988223995256 0.24219822803104135
chr17 81195210 3282605 0.04042855483716342 0.2614423086013911
chr18 78077248 2589101 0.033160761506348176 0.7433925945295861
chr19 59128983 2287803 0.0386917359968799 0.41037145499721184
chr20 63025520 2557238 0.040574643414286786 0.23407838178182236
chr21 48129895 1521685 0.03161621275093162 0.21878684742955767
chr22 51304566 1365334 0.02661232920282378 0.17885997786302343
chrMT 16571 9142 0.5516866815521091 0.7875796104957745
chrX 155270560 7478231 0.04816258149645367 0.2713064141428936
chrY 59373566 317664 0.005350259743536374 0.13975920937792077