I have aligned my reads using BWA mem. I ran CollectAlignmentSummaryMetrics using picard.jar

I obtained following summary:

## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectAlignmentSummaryMetrics REFERENCE_SEQUENCE=lyrata_genome.fa INPUT=aligned_MA605readsBWA.bam OUTPUT=alignmentsummaryMA605-bam.txt    MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
## htsjdk.samtools.metrics.StringHeader
# Started on: Sun Sep 27 23:49:34 EDT 2015

## METRICS CLASS    picard.analysis.AlignmentSummaryMetrics
CATEGORY    TOTAL_READS    PF_READS    PCT_PF_READS    PF_NOISE_READS    PF_READS_ALIGNED    PCT_PF_READS_ALIGNED    PF_ALIGNED_BASES    PF_HQ_ALIGNED_READS    PF_HQ_ALIGNED_BASES    PF_HQ_ALIGNED_Q20_BASES    PF_HQ_MEDIAN_MISMATCHES    PF_MISMATCH_RATE    PF_HQ_ERROR_RATE    PF_INDEL_RATE    MEAN_READ_LENGTH    READS_ALIGNED_IN_PAIRS    PCT_READS_ALIGNED_IN_PAIRS    BAD_CYCLES    STRAND_BALANCE    PCT_CHIMERAS    PCT_ADAPTER    SAMPLE    LIBRARY    READ_GROUP
FIRST_OF_PAIR    11096513    11096513    1    0    10688222    0.963205    932254588    7349970    641058986    634880748    0    0.009054    0.00862    0.000889    89.052548    10619392    0.99356    0    0.499903    0.021993    0            
SECOND_OF_PAIR    11096513    11096513    1    0    10692315    0.963574    941634434    7353634    647175477    644184510    0    0.008256    0.007826    0.000889    89.889588    10619392    0.99318    0    0.500354    0.021993    0            
PAIR    22193026    22193026    1    0    21380537    0.96339    1873889022    14703604    1288234463    1279065258    0    0.008653    0.008221    0.000889    89.471068    21238784    0.99337    0    0.500129    0.021993    0

I see that there has been report of ADAPTER_SEQUENCE . Does it mean that my aligned reads still has adapters left over? I guess is not, but want to confirm. Also, how to get a clear and useful summary of my alignment? I want something like:

How much reads (# and %) have aligned to my reference genome?

How much read (# and %) have not aligned to my reference genome? Is there a way to retain the unmapped reads (BWA or BOWTIE2)?

Thanks in advance!

-Bishwa K.