Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,556,190	C→T	V31I (GTC→ATC)	bdm ←	biofilm‑dependent modulation protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,556,190	0	C	T	98.7%	261.7 / ‑4.5	77	V31I (GTC→ATC)	bdm	biofilm‑dependent modulation protein
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (44/32);  total (44/33)
Fisher's exact test for biased strand distribution p-value = 4.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01

TAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAGTAAACATAG  >  NC_000913/1556096‑1556282                                                                                               |                                                                                             tAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAacac                                                                                         <  2:719251/100‑1 (MQ=255) tAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAacac                                                                                         >  2:1044887/1‑100 (MQ=255) tAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAacac                                                                                         <  2:1742048/100‑1 (MQ=255)  aaTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACAcc                                                                                        >  2:747543/1‑100 (MQ=255)   aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCa                                                                                       <  2:615508/100‑1 (MQ=255)   aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCa                                                                                       <  1:267429/100‑1 (MQ=255)   aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCa                                                                                       <  2:1754580/100‑1 (MQ=255)     tGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATg                                                                                     >  1:738057/1‑100 (MQ=255)      gATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGc                                                                                    >  2:413589/1‑100 (MQ=255)      gATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGc                                                                                    <  1:367274/100‑1 (MQ=255)       aTCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCt                                                                                   >  1:208351/1‑100 (MQ=255)         cGTTTGCTGGTAGATATCACTGATGATGTCGGTATCAGTATCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATTCtgt                                                                                 >  1:1176611/1‑100 (MQ=255)         cGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCtgt                                                                                 <  1:572360/100‑1 (MQ=255)          gTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCtgtg                                                                                <  2:321837/100‑1 (MQ=255)           tttGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGc                                                                               <  1:198856/100‑1 (MQ=255)              gCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTAAGTGATAACACCATGCTGTGCCCg                                                                            >  2:171749/1‑100 (MQ=255)              gCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTACATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGccc                                                                             >  1:269721/1‑99 (MQ=255)                 ggTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTAAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCACGa                                                                           >  1:425344/1‑98 (MQ=255)                  gTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAgg                                                                        >  2:1369262/1‑100 (MQ=255)                   tAGATATCACTGAGGATGTCGTTATCAGAAGCTTCATCCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGc                                                                       <  2:1532592/100‑1 (MQ=255)                     gATATCACTGAGGATGTTGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCt                                                                     <  2:540471/100‑1 (MQ=255)                     gATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCt                                                                     <  2:399654/100‑1 (MQ=255)                        atCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGc                                                                  <  2:38979/100‑1 (MQ=255)                               aGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAAt                                                             <  1:877306/98‑1 (MQ=255)                                   tGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGACTTGCTCAATGGCAtt                                                       >  2:98597/1‑100 (MQ=255)                                     tCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTaa                                                     >  2:290797/1‑100 (MQ=255)                                         tATCAGACGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCGGTGCCCGAAGGCCTTGCTCAATGGCATTAACCag                                                 >  1:955606/1‑100 (MQ=255)                                            cAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGc                                              <  1:751991/100‑1 (MQ=255)                                             aGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCg                                             >  2:1100423/1‑100 (MQ=255)                                             aGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCg                                             >  2:737287/1‑100 (MQ=255)                                                   ttCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTct                                       >  2:489996/1‑100 (MQ=255)                                                   ttCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTc                                        <  1:1217507/99‑1 (MQ=255)                                                        cccATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACAAGAGAGGGTTATGCTGt                                  >  2:70893/1‑100 (MQ=255)                                                          cATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTg                                <  1:1513917/100‑1 (MQ=255)                                                          cATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCACGAACGCCTTGCTCAATGGCATTAAACAGAGCGGGTTCTGCTGtt                                 >  1:812581/1‑99 (MQ=255)                                                            tttGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGaa                              <  2:1201949/100‑1 (MQ=255)                                                              tGGTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAAtt                            >  2:65029/1‑100 (MQ=255)                                                               ggTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAAttt                           >  2:978585/1‑100 (MQ=255)                                                               ggTCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAAttt                           <  2:1658890/100‑1 (MQ=255)                                                                 tCAGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTc                         <  1:1508152/100‑1 (MQ=255)                                                                   aGCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTg                       <  1:171749/100‑1 (MQ=255)                                                                    gCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGc                      <  2:1061732/100‑1 (MQ=255)                                                                    gCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGc                      >  2:321403/1‑100 (MQ=255)                                                                    gCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGc                      >  1:1589288/1‑100 (MQ=255)                                                                    gCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGc                      >  2:792248/1‑100 (MQ=255)                                                                    gCTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCACGAAGGACTTGCTCAATGGCATTAAACAGAGCGGGCTCTGCTGTTGAATTTTCt                        >  1:576226/1‑98 (MQ=255)                                                                     cTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGcc                     >  1:410154/1‑100 (MQ=255)                                                                     cTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGcc                     <  1:1740554/100‑1 (MQ=255)                                                                     cTCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGcc                     <  1:1100413/100‑1 (MQ=255)                                                                      tCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGc                      >  2:1635748/1‑98 (MQ=255)                                                                      tCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCt                    >  1:441230/1‑100 (MQ=255)                                                                      tCCATGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCt                    >  2:1769648/1‑100 (MQ=255)                                                                        cATGATAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAATGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGa                  <  1:320401/100‑1 (MQ=255)                                                                          tGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGata                <  2:208352/100‑1 (MQ=255)                                                                          tGAGAATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAACGAGTTCTGCTGTTAAATTTTCTGCCTGata                >  2:420629/1‑100 (MQ=255)                                                                          tGAGAATGTCATCTTCAGTGACAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGata                <  1:222098/100‑1 (MQ=255)                                                                           gagaATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGataa               <  1:1046389/100‑1 (MQ=255)                                                                            agaATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGataat              >  1:1809558/1‑100 (MQ=255)                                                                            agaATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGataat              >  1:847569/1‑100 (MQ=255)                                                                            agaATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGataat              >  2:1176737/1‑100 (MQ=255)                                                                            agaATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGataat              >  2:495314/1‑100 (MQ=255)                                                                             gaATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGataata             <  1:1396380/100‑1 (MQ=255)                                                                             gaATGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGataata             >  1:233463/1‑100 (MQ=255)                                                                               aTGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAg           <  2:236940/100‑1 (MQ=255)                                                                               aTGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAg           <  1:413587/100‑1 (MQ=255)                                                                                tGTCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAGt          >  2:1177432/1‑100 (MQ=255)                                                                                  tCATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAGTaa        >  1:1289295/1‑100 (MQ=255)                                                                                   cATCTTCTGTGATAACACGATGATGTGACCGAAGGACTTGCTGAATGGCATTAACGAGAGCGGGTTCTGCTGTTGAATTTTATGCCTGATAATAATTaaa       >  1:419004/1‑100 (MQ=255)                                                                                   cATCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAGTaaa       <  2:912315/100‑1 (MQ=255)                                                                                     tCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAGTAAACa     >  1:1331935/1‑100 (MQ=255)                                                                                     tCTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAGTAAACa     >  1:1169535/1‑100 (MQ=255)                                                                                      cTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAGTAAACAt    >  2:571983/1‑100 (MQ=255)                                                                                      cTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAGTAAACAt    >  2:572157/1‑100 (MQ=255)                                                                                      cTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAGTAAACAt    >  1:761910/1‑100 (MQ=255)                                                                                      cTTCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAGTAAACAt    >  1:398096/1‑100 (MQ=255)                                                                                       ttCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAGTAAACATa   >  1:1815628/1‑100 (MQ=255)                                                                                        tCAGTGATAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAGTAAACATAg  <  1:1032319/100‑1 (MQ=255)                                                                                               |                                                                                             TAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGTCATCTTCAGTGACAACACCATGCTGTGCCCGAAGGCCTTGCTCAATGGCATTAACCAGAGCGGGTTCTGCTGTTGAATTTTCTGCCTGATAATAAGTAAACATAG  >  NC_000913/1556096‑1556282

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑