Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,735,446	C→T	24.9%	T23T (ACC→ACT)	sodB →	superoxide dismutase, Fe

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,735,446	0	C	T	24.9%	126.1 / 43.5	77	T23T (ACC→ACT)	sodB	superoxide dismutase, Fe
Reads supporting (aligned to +/- strand):  ref base C (34/23);  new base T (10/9);  total (45/32)
Fisher's exact test for biased strand distribution p-value = 6.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.27e-01

GTATGCAAATTAATAATAAAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGTTTGAAGGTAAATCACTGGAAGAGAT  >  NC_000913/1735347‑1735544                                                                                                    |                                                                                                   gTATGCAAATTAATAATAAAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAAcc                                                                                                    <  1:1566242/100‑1 (MQ=255)  tATGCAAATTAATAATAAAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCa                                                                                                   >  1:1954104/1‑100 (MQ=255)   aTGCAAATTAATAATAAAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCAt                                                                                                  >  1:1433118/1‑100 (MQ=255)     gCAAATTAATAATAAAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCg                                                                                                <  2:470271/100‑1 (MQ=255)     gCAAATTAATAATAAAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCg                                                                                                <  2:1674008/100‑1 (MQ=255)     gCAAATTAATAATAAAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCg                                                                                                <  2:1327745/100‑1 (MQ=255)         aTTAATAATAAAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTa                                                                                            >  1:1967491/1‑100 (MQ=255)           taataataaAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATc                                                                                          >  2:1615846/1‑100 (MQ=255)           taataataaAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATc                                                                                          <  1:723341/100‑1 (MQ=255)            aataataaAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCa                                                                                         <  2:1401839/100‑1 (MQ=255)            aataataaAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCa                                                                                         <  1:513932/100‑1 (MQ=255)             ataataaAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCAc                                                                                        <  1:1638830/100‑1 (MQ=255)              taataaAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACt                                                                                       >  1:406048/1‑100 (MQ=255)               aataaAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCTGAAACTATCGAGTATCACTa                                                                                      >  2:2096649/1‑100 (MQ=255)               aataaAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACTATCGAGTATCACTa                                                                                      >  1:1731013/1‑100 (MQ=255)               aataaAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACt                                                                                       >  2:542198/1‑99 (MQ=255)                 taaAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACTATCGAGTATCACTACg                                                                                    <  1:797961/100‑1 (MQ=255)                   aaGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACTATCGAGTATCACTACGGc                                                                                  <  2:351047/100‑1 (MQ=255)                     ggAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACTATCGAGTATCACTACGGCaa                                                                                >  1:103300/1‑100 (MQ=255)                     ggAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCaa                                                                                >  1:233854/1‑100 (MQ=255)                        gagTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACTATCGAGTATCACTACGGCAAGCa                                                                             >  1:570880/1‑100 (MQ=255)                        gagTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCa                                                                             >  1:507018/1‑100 (MQ=255)                         agTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCAc                                                                            >  1:2184612/1‑100 (MQ=255)                          ntAGCAATGTTATTAGAATTAACTGAACTACCATATGCTAAAGATGCTATGGCACTGCACCATTCTGCGGACAAAATCGAGTATCAATAAGGCAAGCa                                                                             >  2:661554/2‑98 (MQ=255)                          gTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACTATCGAGTATCACTACGGCAAGCAcc                                                                           <  1:618463/100‑1 (MQ=255)                          gTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCAcc                                                                           <  2:580527/100‑1 (MQ=255)                               aaTGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAg                                                                      <  1:1878578/100‑1 (MQ=255)                                 tGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGAc                                                                    <  1:2119969/100‑1 (MQ=255)                                    cATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTa                                                                 >  2:1891101/1‑100 (MQ=255)                                        cGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACTATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTc                                                             >  2:1071683/1‑100 (MQ=255)                                        cGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTc                                                             >  1:578657/1‑100 (MQ=255)                                              aCCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACTATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAAc                                                       >  1:2070781/1‑100 (MQ=255)                                               ccTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAAcc                                                      >  1:2152502/1‑100 (MQ=255)                                               ccTGCACTACCATATGCTAAAGATGATCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAAcc                                                      >  2:996960/1‑100 (MQ=255)                                                cTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCt                                                     >  1:1072478/1‑100 (MQ=255)                                                cTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGAGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCt                                                     >  1:1006384/1‑100 (MQ=255)                                                 tGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTg                                                    <  2:62017/100‑1 (MQ=255)                                                  gCACTACCATATGCTAAAGATGCTCTTGCACCGCACATTGCTGCGGAAACTATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGa                                                   <  2:451898/100‑1 (MQ=255)                                                   cACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACTATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGaa                                                  <  1:3548/100‑1 (MQ=255)                                                   cACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCATACTTATGTCACTAACCTGaa                                                  <  2:1004722/100‑1 (MQ=255)                                                       aCCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGa                                                   <  1:68266/95‑1 (MQ=255)                                                       aCCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCACCAGACTTATGTCACTAACCTGaacaac                                              >  2:1641808/1‑100 (MQ=255)                                                         cATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACTATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGACCAACCt                                            >  1:555246/1‑100 (MQ=255)                                                          ntatGCTAAAGATGCTATGGCAACGCACATTTCTGCGGAAACCATCGAGTATAACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCt                                            >  2:864259/2‑99 (MQ=255)                                                          atatGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTg                                           >  1:1355875/1‑100 (MQ=255)                                                           tatGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACTATCGAGTATCACTACGGCAAGCACCATCAGACTTACGTCACTAACCTGAACAACCTGa                                          <  2:1298447/100‑1 (MQ=255)                                                            atGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGAt                                         >  2:228798/1‑100 (MQ=255)                                                              gCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACTATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAAACTGAACAACCTg                                           >  2:1354795/1‑96 (MQ=255)                                                              gCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTa                                       >  1:1954377/1‑100 (MQ=255)                                                              gCTAAAGATGCTCTGGCACCGCAAATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATAAGACGTATGTCACTAACCGGAACAACCTGAtt                                        >  2:204849/1‑99 (MQ=255)                                                               cTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGAtt                                        <  2:507019/98‑1 (MQ=255)                                                               cTAAAGATGCACTGGCACCGCACATTTCTGCGGAAACTATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTaa                                      >  2:1579127/1‑100 (MQ=255)                                                                tAAAGATGCTCTGGCACCGCACATTTCAGCGGAAACCATCGAGCATCACTACGGCAAGCACCATTAGACGCATGTCACTAACCTGAACACCCCGAt                                         >  2:279524/1‑96 (MQ=255)                                                                tAAAGATGCTCTGGCACCGCAAATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTaaa                                     <  1:801344/100‑1 (MQ=255)                                                                 aaaGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGCCTTATGTCACTAACCTGAACAACCTGATTaaa                                     >  2:198407/1‑99 (MQ=255)                                                                 aaaGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAg                                    >  1:1293637/1‑100 (MQ=255)                                                                    gATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTa                                 >  1:1327929/1‑100 (MQ=255)                                                                      tGCTCTGGCACCGCACATTTCTGCGGAAACTATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCCCTAACCTGAACAAACTGATTAAAGGTAc                                >  1:2211314/1‑99 (MQ=255)                                                                        ctctGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACcgc                             >  1:960224/1‑100 (MQ=255)                                                                          ctGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGt                           >  1:1028198/1‑100 (MQ=255)                                                                          ctGGCACCGCACATTTCTGCGGAAACCATCAAGCATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAACGGTACCGCGt                           >  2:1474770/1‑100 (MQ=255)                                                                            gtgactgCACATTGCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTGTGTCACTACCCTGAACAACCTGATTAAAGGTACCGCGttt                         <  2:683180/94‑1 (MQ=255)                                                                            ggCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGttt                         >  2:91866/1‑100 (MQ=255)                                                                            ggCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGttt                         <  1:805504/100‑1 (MQ=255)                                                                            ggCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGttt                         <  2:82692/100‑1 (MQ=255)                                                                             gCACCGCACATTTCTGCGGAAACTATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGTTTg                        <  1:290796/100‑1 (MQ=255)                                                                               aCCGCACATTTCTGCGGAAACCATCGAGTGTTACTACGGCAAGCACCATCAGACTTATGTCATTAACCTGAACATCCTGATTAAAGGTACCGCGTTTg                        <  2:979144/98‑1 (MQ=255)                                                                                 cGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGTTTGAAgg                    <  2:1862055/100‑1 (MQ=255)                                                                                 cGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGTTTGAAg                     <  1:2093465/99‑1 (MQ=255)                                                                                   cacaTTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGTTTGAAGGTa                  >  2:642043/1‑100 (MQ=255)                                                                                      aTTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGTTTGAAGGTAAAt               >  1:656912/1‑100 (MQ=255)                                                                                             cGGAAACTATCGAGTATCACTACGGCAAGCACCATCAGACTTATTTCACTAACCTGAACAACCTGATTAAAGGTACCGCGTTTGAAGGTAAATCACTGGa        <  2:995702/100‑1 (MQ=255)                                                                                             cGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGTTTGAAGGTAAATCACTGGa        <  2:2230610/100‑1 (MQ=255)                                                                                             cGGAAACCATCGAGTATCACTACGGCAAGCACCATCAAACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGTTTGAAGGTAAATCACTGGa        >  2:1192816/1‑100 (MQ=255)                                                                                              ggAAACTATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGTTTGAAGGTAAATCACTGGaa       <  2:126711/100‑1 (MQ=255)                                                                                              ggAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGTTTGAAGGTAAATCACTGGaa       <  1:570150/100‑1 (MQ=255)                                                                                                  aCCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGTTTGAAGGTAAATCACTGGAAgaga   >  2:1399017/1‑100 (MQ=255)                                                                                                  aCCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGTTTGAAGGTAAATCACTGGAAgaga   >  2:278822/1‑100 (MQ=255)                                                                                                   ccATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGTTTGAAGGTAAATCACTGGAAGAGat  >  2:697205/1‑100 (MQ=255)                                                                                                    |                                                                                                   GTATGCAAATTAATAATAAAGGAGAGTAGCAATGTCATTCGAATTACCTGCACTACCATATGCTAAAGATGCTCTGGCACCGCACATTTCTGCGGAAACCATCGAGTATCACTACGGCAAGCACCATCAGACTTATGTCACTAACCTGAACAACCTGATTAAAGGTACCGCGTTTGAAGGTAAATCACTGGAAGAGAT  >  NC_000913/1735347‑1735544

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑