Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,019,309	C→A	27.8%	D249Y (GAT→TAT)	ompA ←	outer membrane porin A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,019,309	0	C	A	27.8%	55.8 / 17.7	43	D249Y (GAT→TAT)	ompA	outer membrane porin A
Reads supporting (aligned to +/- strand):  ref base C (18/13);  new base A (7/5);  total (25/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

GAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTCCGGTGCCGGAGCTGGAGC  >  NC_000913/1019167‑1019447                                                                                                                                               |                                                                                                                                           gagaTCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATc                                                                                                                                            >  2:128673/1‑143 (MQ=255) agtaTCTTGTCTCCCGGGAGTCCTTTGGATATCAGGTAATAAATAACAGGCTGAGCACGGCGCTCGGACAGGCCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATc                                                                                                                                            <  2:614469/140‑1 (MQ=255)   gaTTTTGTCGGGCGGGATGCCGTTGGGGACCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCa                                                                                                                                          <  2:570068/143‑1 (MQ=255)      ctggTCTGCCGGGATGCCTTTGGGGATCAGGTAGTCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGATCCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGt                                                                                                                                       <  2:588993/140‑1 (MQ=255)      ctcgccTGCCGGGATACCTTTGGAGATCAGGTAAGCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATACAGGt                                                                                                                                       <  1:93832/138‑1 (MQ=255)              ccGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAgc                                                                                                                               <  1:837174/143‑1 (MQ=255)                 ggATACCTGTGGAGGTCAGGTAAGCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAgctgg                                                                                                                            <  2:847952/143‑1 (MQ=255)                         ttGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTAAGGAACCGTCTTTCGGATACAGGTTGCTCAGATGGCTGTATAg                                                                                                                    >  1:482203/1‑143 (MQ=255)                           ggAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCt                                                                                                                  <  1:20319/143‑1 (MQ=255)                                 catgTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCa                                                                                                            <  2:467475/140‑1 (MQ=255)                                 cAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCa                                                                                                            >  1:619031/1‑143 (MQ=255)                                 cAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGCACAGCTGATcgg                                                                                                            >  1:141360/1‑141 (MQ=255)                                   gttattCAACAACAGTCTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCaga                                                                                                          <  2:813113/138‑1 (MQ=255)                                   ggTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCaga                                                                                                          <  1:61732/143‑1 (MQ=255)                                         caacaaCAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATACAGGTTGCTCCCCTGGCTGTCCAGCTGCTCCAGAGCAGcc                                                                                                    >  1:237704/1‑143 (MQ=255)                                          aacaacAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGGTCCAGAGCAGCCt                                                                                                   >  2:702172/1‑143 (MQ=255)                                          aacaacAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGCATCCAGGTTGCTCAGCTGGCTGTACAGCCGCTCCGGGgccgccg                                                                                                   >  2:708011/1‑142 (MQ=255)                                                    tGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATACAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCgg                                                                                         >  1:143554/1‑143 (MQ=255)                                                           ggCGCTCGGACACACCCTGGTTGTAAGCGTGAGACCCGATGCGGTCGGTGTAACCCAGAACGACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAgg                                                                                  <  2:804406/143‑1 (MQ=255)                                                                  ggACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGTCTGACCTTCCGGTTTCAGGGTTGCtt                                                                           <  1:128673/143‑1 (MQ=255)                                                                    aCAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGATttg                                                                         >  1:546731/1‑143 (MQ=255)                                                                         cccTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTgttgaa                                                                    <  1:730513/143‑1 (MQ=255)                                                                                     gCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAAc                                                        >  2:385068/1‑143 (MQ=255)                                                                                       gTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATACAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCt                                                                                                   >  1:430638/1‑98 (MQ=255)                                                                                       gTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATACAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCt                                                                                                   <  2:430638/98‑1 (MQ=255)                                                                                         cAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCa                                                    >  1:397013/1‑143 (MQ=255)                                                                                          aGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCCGCGCAGCCTGACCCTCCGGTTTCAGGGTTGCGTTGTTGAAGTTGAACAGAACGTCAg                                                   >  1:458578/1‑143 (MQ=255)                                                                                          aGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTGGCTTTGTTGAAGATGCACAGAAcagcag                                                   >  2:495381/1‑138 (MQ=255)                                                                                                        cggtGTATCTCAGATCAACTTCGGAACCGTCTTTCGGATACAGTTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAg                                     <  1:228471/143‑1 (MQ=255)                                                                                                         ggtGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGt                                    >  2:494493/1‑143 (MQ=255)                                                                                                             tAACCCAGAACAACTACGGAACCGTCTTTCGGATACAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCtt                                <  2:615999/143‑1 (MQ=255)                                                                                                              aacggaGAACGACTACGGAACCGCCTGTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACGGAACGTCAGACTTCAGAGTGAAGTGCTTg                               <  1:872717/138‑1 (MQ=255)                                                                                                               aCCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTgg                              >  2:616406/1‑143 (MQ=255)                                                                                                                cccAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGGTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCGGACTTCAGGGTGAAGTGCTTGGt                             >  1:420494/1‑143 (MQ=255)                                                                                                                 ccAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAACAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTCGGTGGTGGACCGAACATCTGACCTCAGAGTGAAGTGCTTGGTc                            >  1:647258/1‑143 (MQ=255)                                                                                                                         accgcGGACCCGTCTTGCGGTGCCGGGTTGCTCAGCTGGCTGCACAGCTGATCCAGAGCAGCCTGAGCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTc                    <  2:157314/139‑1 (MQ=255)                                                                                                                          caagggAACCGTCTTTCGGAGACAGGTGGGTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTcc                   <  1:705869/139‑1 (MQ=255)                                                                                                                          cTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAAGGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTcc                   >  1:363739/1‑143 (MQ=255)                                                                                                                           tACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGAACCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTCCg                  >  1:193451/1‑143 (MQ=255)                                                                                                                           tACGGAACCGTCTTTCGGATACAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACGTGAGAGTGAAGTGCTTGGGCTCTCCTTCCg                  >  2:611669/1‑143 (MQ=255)                                                                                                                                    gTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTAAGACATCAGAGTGAAGTGCTTGGTCTGTACTTGCGGTGCCGGAg         >  2:54885/1‑143 (MQ=255)                                                                                                                                     tCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTCCGGTGCCGGAGc        >  1:825838/1‑143 (MQ=255)                                                                                                                                         tCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTCCGGTGCCGGAGCTGGa    >  1:877597/1‑143 (MQ=255)                                                                                                                                          cGGATACAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTCCGGCGCCGGAGCTGGAg   >  1:821671/1‑143 (MQ=255)                                                                                                                                           ggATACAGGTTGCTCAGCTGGCTGTAAAGCTGAACCAGAGCAGCCTGACCTTCCGGTTTCAGGGATGCGTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTCCAGTGGCGGAGAGGGAGc  >  2:379492/1‑143 (MQ=255)                                                                                                                                               |                                                                                                                                           GAGATCTTGTCTGCCGGGATACCTTTGGAGATCAGGTAATCAACAACAGACTGAGCACGGCGCTCGGACAGACCCTGGTTGTAAGCGTCAGAACCGATGCGGTCGGTGTAACCCAGAACAACTACGGAACCGTCTTTCGGATCCAGGTTGCTCAGCTGGCTGTACAGCTGATCCAGAGCAGCCTGACCTTCCGGTTTCAGGGTTGCTTTGTTGAAGTTGAACAGAACGTCAGACTTCAGAGTGAAGTGCTTGGTCTGTACTTCCGGTGCCGGAGCTGGAGC  >  NC_000913/1019167‑1019447

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑