Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,839,499	T→C	L165L (TTA→TTG)	nlpA ←	lipoprotein‑28

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,839,499	0	T	C	97.8%	150.8 / NA	45	L165L (TTA→TTG)	nlpA	lipoprotein‑28
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (26/18);  total (27/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAATGTAAGTGGTGCTGATAATCGCTACATCAACTTTGGGATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGTAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGATTTTTT  >  NC_000913/3839372‑3839635                                                                                                                                |                                                                                                                                         gAATGTAAGTGGTGCTGATAATCGCTACATCAACTTTGGGATCATCCAGTACGCGCGGGAGCTACGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCtttt                                                                                                                              <  2:73441/140‑1 (MQ=255)   aTGTAAGTGGTGCTGATAATCGCTACATCAACTTTGGGATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTcc                                                                                                                            <  2:658413/140‑1 (MQ=255)            gtgCTGATAATCGCTACATCAACTTTGGGATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTccc                                                                                                                           >  1:562254/1‑132 (MQ=255)            gtgCTGATAATCGCTACATCAACTTTGGGATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTccc                                                                                                                           <  2:562254/132‑1 (MQ=255)            gtgCTGATAATCGCTACATCAACTTTGGGATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCag                                                                                                                   <  2:672276/140‑1 (MQ=255)               cTGATAATCGCTACATCAACTTTGGGATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGt                                                                                                                >  2:105732/1‑140 (MQ=255)                       cGCTACATCAACTTTGGGATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCt                                                                                                        >  1:443646/1‑140 (MQ=255)                          tACATCAACTTTGGGATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGTAATAACCTTTTTCCATCTTTCGGAGTAATTAGCTtct                                                                                                     >  1:297879/1‑140 (MQ=255)                                  cTTTGGGATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGc                                                                                             <  1:608322/140‑1 (MQ=255)                                  cTTTGGGATCATCCACTACGCGAGGCAGCTGCGCCCCATCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGc                                                                                             <  1:385791/140‑1 (MQ=255)                                    ttGGGATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCaa                                                                                           <  2:683388/140‑1 (MQ=255)                                      gggATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACa                                                                                         >  1:33501/1‑140 (MQ=255)                                      gggATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACa                                                                                         >  2:811236/1‑140 (MQ=255)                                      gggATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACa                                                                                         >  2:418656/1‑140 (MQ=255)                                      gggATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTGTTCACTCGTTCAGAGTCATTAGCTTCTCTTTTTGCAACa                                                                                         >  2:278350/1‑140 (MQ=255)                                        gATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGt                                                                                       >  2:814954/1‑140 (MQ=255)                                            atcCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTaaaa                                                                                   >  1:59711/1‑140 (MQ=255)                                            atcCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCATTCAGAGTAATTAGATTCTCTTTTTGCAACAGTaaaa                                                                                   >  1:276056/1‑140 (MQ=255)                                                   aCGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGcgcg                                                                            >  1:105550/1‑140 (MQ=255)                                                    cgcgcgGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTgc                                                                               >  1:736525/1‑136 (MQ=255)                                                    cgcgcgGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTgc                                                                               <  2:736525/136‑1 (MQ=255)                                                      cgcgGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGAcc                                                                         >  2:711088/1‑140 (MQ=255)                                                                   cccccTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTggtcggg                                                            <  1:814954/140‑1 (MQ=255)                                                                      ccTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTggtcgggtcg                                                         <  1:811236/140‑1 (MQ=255)                                                                           aGTTCCATAATCTGCCAATGACCAGGATTATCGGTTAAATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTggg                                                    <  1:278350/140‑1 (MQ=255)                                                                            gTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTgggg                                                   <  1:418656/140‑1 (MQ=255)                                                                                  tAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGAAACAGTAATAGTCCGCCACCAAGGTAGGTCGGGTCGTTGGGGATCGcc                                             >  2:256498/1‑140 (MQ=255)                                                                                  tAATCTGCAAATGACGAGGATTATCGATTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGcc                                             >  1:684488/1‑140 (MQ=255)                                                                                        gCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTc                                       >  2:257821/1‑140 (MQ=255)                                                                                          aaaTGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTcgc                                     >  1:406907/1‑140 (MQ=255)                                                                                           aaTGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAGCAGTAAAAGTGCGCGACGAAGGTTGGTCGGGTCGTTGGGAATCGCCACTGTcgcg                                    >  1:258511/1‑140 (MQ=255)                                                                                           aaTGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTcgcg                                    >  1:553324/1‑140 (MQ=255)                                                                                            aTGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCgcgc                                   <  1:257821/140‑1 (MQ=255)                                                                                            aTGACGAGGATTATCGGTTATACCCGGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCgcgc                                   <  1:275036/140‑1 (MQ=255)                                                                                            aTGACGAGGATTATCGATTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCgcgc                                   <  2:684488/140‑1 (MQ=255)                                                                                             tGACGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGcc                                  <  1:808246/140‑1 (MQ=255)                                                                                                cGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTc                                       >  1:15773/1‑132 (MQ=255)                                                                                                cGAGGATTATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTc                                       <  2:15773/132‑1 (MQ=255)                                                                                                      ttATCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGACGGGTCGCTGGGGATCCCCACAGTCGCGCCTTCTTTTAt                         >  2:293727/1‑140 (MQ=255)                                                                                                        aTCGGTTATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTAttt                       >  1:452365/1‑140 (MQ=255)                                                                                                             ttATATCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACC‑AGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCa                 <  1:5391/140‑1 (MQ=255)                                                                                                              tataTCCAGCGCGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGATCGGGTCGCTGGAGATCGCCACTGTAGCGCTTTCTTTTATTTGCGCCa                 >  2:374023/1‑140 (MQ=255)                                                                                                                      gcgcGGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTg         >  2:87612/1‑140 (MQ=255)                                                                                                                       cgcgGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGTAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCGACTGTCGGGCCGTCTTTTATTTGCGCCACGGTTTTGa        >  1:349606/1‑140 (MQ=255)                                                                                                                       cgcgGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGa        >  2:740312/1‑140 (MQ=255)                                                                                                                       cgcgGTAGGCAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGCTGGGGATCCCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGa        >  2:273162/1‑140 (MQ=255)                                                                                                                          ggtaggcaATAACCCCTTTCCCCCTATCAAAGTAATTGGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGAttt     <  1:256498/140‑1 (MQ=255)                                                                                                                            taggcaATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTGTAGTTGCGCTACGGTTTTGAttttt   >  1:380745/1‑140 (MQ=255)                                                                                                                             aggcaATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCCTTTATTTGCGCCACGGTTTTGAtttttt  <  1:813684/140‑1 (MQ=255)                                                                                                                                |                                                                                                                                         GAATGTAAGTGGTGCTGATAATCGCTACATCAACTTTGGGATCATCCAGTACGCGCGGGAGCTGCGCCCCCTCGAGTTCCATAATCTGCAAATGACGAGGATTATCGGTTATATCCAGCGCGGTAGGTAATAACCCTTTTCCCTCTTTCAGAGTAATTAGCTTCTCTTTTTGCAACAGTAAAAGTGCGCGACCAAGGTTGGTCGGGTCGTTGGGGATCGCCACTGTCGCGCCTTCTTTTATTTGCGCCACGGTTTTGATTTTTT  >  NC_000913/3839372‑3839635

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑