Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	560,243	0	A	G	22.4%	108.1 / 27.9	58	N183D (AAT→GAT)	sfmD	putative outer membrane export usher protein
Reads supporting (aligned to +/- strand):  ref base A (29/16);  new base G (7/6);  total (36/22)
Fisher's exact test for biased strand distribution p-value = 5.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.22e-01

CCTGAACATCACTATTCCTCAGATAGCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTAATATTGGCCCGTGGCGTTTACGCAACAA  >  NC_000913/560146‑560340                                                                                                  |                                                                                                  ccTGAACATCACTATTCCTCAGATAGCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAAt                                                                                                 <  1:843304/100‑1 (MQ=255) ccTGAACATCACTATTCCTCAGATAGCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAAt                                                                                                 >  1:1139760/1‑100 (MQ=255) ccTGAACATCACTATTCCTCAGATAGCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAAt                                                                                                 >  1:1139949/1‑100 (MQ=255) ccTGAACATCACTATTCCTCAGATAGCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAAt                                                                                                 >  1:1140257/1‑100 (MQ=255)         tCACTATTCCTCAGATAGCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTTGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAAttt                                                                                         >  2:391912/1‑100 (MQ=255)         tCACTATTCCTCAGATAGCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAAttt                                                                                         >  2:1268542/1‑100 (MQ=255)           aCTATTCCTCAGATAGCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCa                                                                                       <  1:941820/100‑1 (MQ=255)             tATTCCTCAGATAGCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCAcc                                                                                     <  1:208083/100‑1 (MQ=255)             atctCCTCAGATAGCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCAcc                                                                                     <  1:1000292/97‑1 (MQ=255)             atctCCTCAGATAGCGTTGTTGAGTAGCGCTCACGGTCACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCAcc                                                                                     <  1:164651/97‑1 (MQ=255)                tCCTCAGATAGCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGt                                                                                  >  1:608710/1‑100 (MQ=255)                tCCTCAGATAGCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGt                                                                                  <  2:183184/100‑1 (MQ=255)                 ccTCAGATAGCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCAccagat                                                                                 >  2:1000283/1‑96 (MQ=255)                 ccTCAGATAGCGTTGTTGAGTAGCGCTCACGGTCACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCAccagat                                                                                 >  2:164649/1‑96 (MQ=255)                         aGCGTTGTTGAGTAGCGCTCACGGTTACATACCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGt                                                                         <  2:441470/100‑1 (MQ=255)                          ncGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTa                                                                        >  2:992707/2‑100 (MQ=255)                          gCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGCGTGGGATGAAGGTATTCCTGCTTTACTCCTGGATTATAATTTCACCGGTAACAGAGGt                                                                         >  2:67777/1‑99 (MQ=255)                          gCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTa                                                                        >  1:1084237/1‑100 (MQ=255)                             ttgttgAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGGATTATAATTTCACCGGTAACAGAGGTAATg                                                                     <  2:895890/100‑1 (MQ=255)                                 tgAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGGATTATAATTTCACCGGTAACAGAGGTAATGGTaa                                                                 >  1:1287807/1‑100 (MQ=255)                                  gAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAAc                                                                >  2:330441/1‑100 (MQ=255)                                   aGTAGCGTTCAAGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAAGTATAATTTCACCGGTAACAGAGGTAATGGTAACg                                                               >  2:687484/1‑100 (MQ=255)                                    gTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGa                                                              >  2:1092555/1‑100 (MQ=255)                                      aGCGCTCACGGTTACATTCCGCCTGAGGAGTGCGATGAACGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATa                                                            <  2:917046/100‑1 (MQ=255)                                      aGCGCTCACGATTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATa                                                            >  2:917811/1‑100 (MQ=255)                                        cgcTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGc                                                          <  2:468107/100‑1 (MQ=255)                                            cACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGGATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTAtt                                                      >  1:926427/1‑100 (MQ=255)                                                 ttACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTAttttttt                                                 <  1:666546/100‑1 (MQ=255)                                                   aCATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATATCTATTTTTTTAg                                               <  1:856315/100‑1 (MQ=255)                                                   aCATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTAttttttttg                                               <  1:878935/100‑3 (MQ=255)                                                       tCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGGATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAg                                           <  2:877672/100‑1 (MQ=255)                                                       tCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGGATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAg                                           <  2:721385/100‑1 (MQ=255)                                                       tCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAg                                           <  1:952155/100‑1 (MQ=255)                                                            cTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTAttttttttttgtgttc                                        >  2:649543/1‑89 (MQ=255)                                                            cTGAAGAGAGGGATGAAGGTATTCCTGCTTTACTCATGGATTATAATTTCACCGGTAACAGAGGTAATGGTATCGATGGATAttttttttttgtt                                           >  2:1051576/1‑89 (MQ=255)                                                             tGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGc                                     >  1:266154/1‑100 (MQ=255)                                                              gAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCg                                    <  1:1190595/100‑1 (MQ=255)                                                                   gTGGGATGAAGGTATTCCTGCTTTACTCCTGGATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGAtt                               <  2:1287796/100‑1 (MQ=255)                                                                   gTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGAt                                >  1:942595/1‑99 (MQ=255)                                                                   gTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGAAACGATAGCTATTTTTTTAGTGAGATcggaagagca                               >  1:610566/1‑91 (MQ=255)                                                                     gggATGAAGGTATTCCTGCTTTACTCCTGGATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTaa                             >  1:1195662/1‑100 (MQ=255)                                                                       gATGAAGGTATTCCTGCTTTACTCCTGGATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGTTCAGCGGGATTAat                            >  2:635244/1‑99 (MQ=255)                                                                         tGAAGGTATTCCTGCTTTACTCCTGGATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTAATAtt                         <  1:1084937/100‑1 (MQ=255)                                                                         tGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTAATAtt                         >  1:36150/1‑100 (MQ=255)                                                                           aaGGTATTCCTGCTTTACTCCTGGATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGTATTCATATTgg                       <  2:687704/100‑1 (MQ=255)                                                                           aaGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTACTGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTAATATTgg                       >  1:947429/1‑100 (MQ=255)                                                                             ggTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTAATATTGGcc                     >  2:752584/1‑100 (MQ=255)                                                                                  tCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTAATATTGGCCCGTgg                >  1:769292/1‑100 (MQ=255)                                                                                    ttccgatcttCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTAATATTGGCCCGTGGCg              <  2:558132/91‑1 (MQ=255)                                                                                     tGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTAATATTGGCCCGTGGCGt             >  2:930672/1‑100 (MQ=255)                                                                                     tGCTTTACTCATGGATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTGAGTGAGCTCAGCGTGATTAATAGTGGCCCGTGGCg              >  2:1218441/1‑99 (MQ=255)                                                                                            cTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTAATATTGGCCCGTGGCGTTTACGca      >  1:1093272/1‑100 (MQ=255)                                                                                             tCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTAATATTGGCCCGTGGCgagatcggaa     >  1:558136/1‑91 (MQ=255)                                                                                              ccTGAATTATTATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGGGGGATTAATATTGGCCCGTGGCGTTTACGcaac    <  2:858178/100‑1 (MQ=255)                                                                                               cTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTAATATTGGCCCGTGGCGTTTACGcaaca   >  1:1161894/1‑100 (MQ=255)                                                                                               cTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTAATATTGGCCCGTGGCGTTTACGcaaca   >  2:140099/1‑100 (MQ=255)                                                                                                tGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTAATATTGGCCCGTGGCGTTTACGcaacaa  >  1:1191477/1‑100 (MQ=255)                                                                                                tGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTAATATTGGCCCGTGGCGTTTACGcaacaa  >  1:929920/1‑100 (MQ=255)                                                                                                  |                                                                                                  CCTGAACATCACTATTCCTCAGATAGCGTTGTTGAGTAGCGCTCACGGTTACATTCCGCCTGAAGAGTGGGATGAAGGTATTCCTGCTTTACTCCTGAATTATAATTTCACCGGTAACAGAGGTAATGGTAACGATAGCTATTTTTTTAGTGAGCTCAGCGGGATTAATATTGGCCCGTGGCGTTTACGCAACAA  >  NC_000913/560146‑560340

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑