BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3080822.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 = 2,539,370
number of mapped reads = 2,160,619 (85.08%)
number of supplementary alignments = 22,059 (0.87%)
number of secondary alignments = 0
number of mapped bases = 146,127,532 bp
number of sequenced bases = 146,072,479 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 182,368
duplication rate = 6.92%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.5815
>>>>>>> ACTG content
number of A's = 42,044,251 bp (28.78%)
number of C's = 26,683,712 bp (18.27%)
number of T's = 46,417,688 bp (31.78%)
number of G's = 30,906,402 bp (21.16%)
number of N's = 20,426 bp (0.01%)
GC percentage = 39.43%
>>>>>>> Mismatches and indels
general error rate = 0.0082
number of mismatches = 1,174,676
number of insertions = 11,283
mapped reads with insertion percentage = 0.52%
number of deletions = 31,311
mapped reads with deletion percentage = 1.43%
homopolymer indels = 47.25%
>>>>>>> Coverage
mean coverageData = 0.0472X
std coverageData = 0.4393X
There is a 3.24% of reference with a coverageData >= 1X
There is a 0.96% of reference with a coverageData >= 2X
There is a 0.3% of reference with a coverageData >= 3X
There is a 0.1% of reference with a coverageData >= 4X
There is a 0.04% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% 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 19288728 0.07738688041222573 0.7534544137690504
chr2 243199373 10875638 0.04471902154122741 0.40745975373480614
chr3 198022430 9804105 0.04951007317706383 0.30224186333369574
chr4 191154276 9060776 0.047400331238208866 0.31035677576789455
chr5 180915260 11111120 0.06141615693446755 0.3385513433338444
chr6 171115067 9859570 0.05761953154014193 0.36525967411883986
chr7 159138663 10486432 0.06589493591510191 0.5247686397526997
chr8 146364022 5036629 0.03441166026443302 0.9596230066948619
chr9 141213431 4752332 0.033653541071457994 0.29176225854270965
chr10 135534747 5478201 0.040419162770119754 0.36110579362400175
chr11 135006516 5687989 0.04213121831838102 0.3025485278053658
chr12 133851895 5305568 0.0396376009469272 0.27242378902590964
chr13 115169878 6580668 0.05713879457265727 0.32996040395698367
chr14 107349540 3068956 0.028588441086938983 0.24294441051065876
chr15 102531392 3712845 0.036211787703028554 0.25710569032998015
chr16 90354753 3116413 0.03449085849418458 0.26472329816727835
chr17 81195210 3598377 0.04431760198661965 0.2979634944333446
chr18 78077248 2075486 0.0265824686853717 0.4671593064868689
chr19 59128983 2196338 0.03714486345892335 0.5484575717006357
chr20 63025520 2429721 0.03855138362999623 0.2706160003282037
chr21 48129895 2542977 0.052835706373346544 0.3255332045786294
chr22 51304566 783342 0.015268465578677734 0.16063854228827515
chrMT 16571 10811 0.6524048035725062 1.0899825773771707
chrX 155270560 8904345 0.057347284636572446 0.33852467526893193
chrY 59373566 360165 0.006066083347596134 0.1410922768669604