Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,689,552	A→G	13.0%	F105S (TTC→TCC)	dnaJ ←	chaperone DnaJ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,689,552	0	A	G	13.0%	121.9 / 6.8	53	F105S (TTC→TCC)	dnaJ	chaperone DnaJ
Reads supporting (aligned to +/- strand):  ref base A (21/23);  new base G (4/3);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 7.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

CGCATGTTACATCTTTACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGCTTGCGCGTTTA  >  CP000730/1689418‑1689686                                                                                                                                       |                                                                                                                                       cGCATGTTACATCTTTACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGaagaaag                                                                                                                                  <  2:534570/141‑1 (MQ=255)   cATGTTACATCTTTACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGaagaaagat                                                                                                                                >  2:263408/1‑140 (MQ=255)              tttACCGATTGAAATTTCTTTTGTTTTACCAAATACCGCTTCTTTAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATc                                                                                                                     <  2:130722/141‑1 (MQ=255)               ttACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCAGCCACCGAAGAAAGAGCTAAAGATATCt                                                                                                                    >  1:482980/1‑141 (MQ=255)                tACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGGAGAAAGAGCTAAAGGTATCtt                                                                                                                   >  1:668209/1‑141 (MQ=255)                tACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGGAGAAAGAGCTAAAGATATCtt                                                                                                                   >  1:550659/1‑141 (MQ=255)                tACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGGAGAAAGAGCTAAAGATATCtt                                                                                                                   >  1:420710/1‑141 (MQ=255)                  cGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCa                                                                                                                 >  1:118/1‑141 (MQ=255)                   ggATTGAACTTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGCCTGCCGCCACCGAAGAAAGAGCTAAAGATATCCTCaa                                                                                                                <  1:474418/141‑1 (MQ=255)                   ggATTGAAATTTCTTTTGTTGTACCAAATACGGCTTCTTCAGATGTTATTGTCCTTTTTTACTGAAGATCATCTCCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCTCCACCGTCGACAGGGCTACAGATCTCTTCaa                                                                                                                >  2:245378/1‑141 (MQ=255)                            tttCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACcgccgc                                                                                                       <  1:491913/141‑1 (MQ=255)                             ttCTTTTGTTGTACCAAATACCGCTTCTTCACATGTTAATGTCATTGTATACGGAAGATCGTCACCTTTGTGCGGTGCATTTGGATCTCTTTGTCTTCCGCCACCGAAGAAAGAGCTAAAGATATCTTCaaaatctctgcc                                                                                                      >  1:25352/1‑133 (MQ=255)                               cTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCAc                                                                                                    <  1:259535/141‑1 (MQ=255)                                    gttgtACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGTTATCTTCAAAACCGCCCCCACCGAAg                                                                                               >  2:572081/1‑141 (MQ=255)                                        tACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGGGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAACCCAc                                                                                           >  1:621020/1‑141 (MQ=255)                                           cAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCTCCTaa                                                                                        >  1:156987/1‑141 (MQ=255)                                             aaTACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACGATTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTaaaa                                                                                      >  2:510162/1‑141 (MQ=255)                                             aaTACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGAATCTCTTTGTCTTCCGCCACCGAAGAAAGAGCCCAAGATATCTTCATATCCGCCGCCACCGCCGCCACGaaac                                                                                      >  2:122356/1‑140 (MQ=255)                                                  cGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCCAAACCGCCGCCCCCCAAGCACCTCAAACcccc                                                                                 >  2:611187/1‑141 (MQ=255)                                                                   aTGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGa                                                                <  1:268067/141‑1 (MQ=255)                                                                    tGTCATTGTATACTGAAGATCATCACATATTTGCGGAGCATTTGGATCTCATTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCCCCGCCACCGAAGCCACTAAAACCGCCAAAAACAAAGCCATTGaa                                                               >  2:658253/1‑141 (MQ=255)                                                                      tCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGCTCCCACTCAAACCGCCAAAGTCAGAGCCATTGAATc                                                             <  1:440608/141‑1 (MQ=255)                                                                       cATTGTTTACTGTAGATCATCTCCTTTTTGAGGTGCATTTGGATCTCTTTGTCCGCCGCCACCGAAGAAAGAGCTAAAGATATCTTTAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATcc                                                            <  2:542224/141‑1 (MQ=255)                                                                          tGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTg                                                         <  1:284739/141‑1 (MQ=255)                                                                          tGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTGTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTg                                                         <  2:447778/141‑1 (MQ=255)                                                                            tataCTGAAGCTCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTc                                                       <  2:481129/141‑1 (MQ=255)                                                                             ataCTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAACCGGCTAAAGTCAGAGCCAGTGAATCCTTGTcc                                                      <  2:635572/141‑1 (MQ=255)                                                                             ataCTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTcc                                                      <  1:430311/141‑1 (MQ=255)                                                                                 cgAAGATCATTCCCTGTTGGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATGGAATCCTTGTccacca                                                  <  1:173843/140‑1 (MQ=255)                                                                                     gATCATCACCTTTTTGCGGTGCATTTGGCTCTCTTTGTCTGCCGCCGCCGAAGCAAGAGCTAAAGATATCTTCAAAACTGGCTCCACCGAAACCACTAAACCCGCCAAAGCCAGATCCATTGAATCCTTGTCAACCACAAc                                              >  1:87849/1‑141 (MQ=255)                                                                                         atcatcTTTTTGCGGCGCATTTGGATCTCTTTGTCTGCCCACACATATAAAAGACGTAGATAGATCTTCAAAGCCGCCTCCACCGAAACCAGTCAAAAAACCCTGGGCCGAACCATTAAATCCGTTTCAACCAAAAcccta                                          >  2:422948/1‑138 (MQ=255)                                                                                         atcaCCTTTTTGCGGCGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGACGCCACTAAAACCACCCAAGTCAGAGCTATTCACTCCTTAACACCCAAAAACttt                                          >  2:292577/1‑140 (MQ=255)                                                                                           caCCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTTTCCACCAACACCTtctg                                        >  2:243016/1‑141 (MQ=255)                                                                                             ccTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGATTCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGa                                      <  1:95528/141‑1 (MQ=255)                                                                                              cTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCCCCGGAGGAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGAc                                     >  1:367943/1‑141 (MQ=255)                                                                                               tttttGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGAcc                                    >  1:401438/1‑141 (MQ=255)                                                                                               tttttGCGGTGCATTTGGATCTCTTTGCCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGCCCACCAAAACCTCGTGGAcc                                    <  1:436050/141‑1 (MQ=255)                                                                                               ttttgGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGAcc                                    <  1:244424/141‑1 (MQ=255)                                                                                                  ttGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACcatc                                 <  2:388004/141‑1 (MQ=255)                                                                                                      ggTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAATGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCTCCAAAGTCAGAGCCATTGAATCCTTGTCCACCATCACCTTGTGGACCATCATGt                             <  1:451575/141‑1 (MQ=255)                                                                                                        tGCAATTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAACGATATCTTCCAAACCGCCCCCACCCAAGCCACCAAAACCGCCCAAATCAGACCCAGCGAATCCGTGTCCCACAAAACCTTAAAGACcatcacgctc                           >  2:461684/1‑136 (MQ=255)                                                                                                          cATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCaa                         >  1:316860/1‑141 (MQ=255)                                                                                                                    tgttttTCTGCCGCCACCGCAGAAAGAGCTAAAGAAATCTTCAAAACCGCCGCCACCCAAGCCACTAAACCCGCCATAGTCAGAGCCATTGCATCCTTGTCCACCAAAACCTTGCGGACCATCATGTCCAAATTGATCATa               <  2:148430/139‑1 (MQ=255)                                                                                                                    cctTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATa               <  1:219/140‑1 (MQ=255)                                                                                                                      tttGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGc             <  2:680806/141‑1 (MQ=255)                                                                                                                         gTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGCTTg          <  1:565503/141‑1 (MQ=255)                                                                                                                          tCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGCTTgc         <  2:524386/141‑1 (MQ=255)                                                                                                                          tCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGCTTgc         <  2:524380/141‑1 (MQ=255)                                                                                                                           cTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCCCCACCGAAGCCACTAAAACCAACAAAGGCAGACCCATAGAATCCATGTCCTCCAAACACTTGTGGACCATAACATCCAAATAAATCACAGCtccac        >  2:268003/1‑137 (MQ=255)                                                                                                                               cgccACCGAAGAAGGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGCCAGAGCCATTGACACCTTGTCCACCAAAACATTGTGGACCTTCATGTCCACCTTTATCaactctacaatctt    >  2:241550/1‑128 (MQ=255)                                                                                                                               cgccACCGAAGAAAGAGCTAGAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAACCCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGGCCAGCATGTCCGAATTGATAATGGCTTGCGCGtt    >  1:139765/1‑141 (MQ=255)                                                                                                                               cgccACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAACCCTTGTCCACCAAAACCTCGTGAACCATCATGTCCAAATTGCACATAGCTTACGGGtt    >  2:340906/1‑141 (MQ=255)                                                                                                                                 ccACCGGAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAATCCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGCTTGCGCGTtta  <  2:420710/141‑1 (MQ=255)                                                                                                                                 ccACCGGAGAAAGAGCTAAAGATACCTCCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGCTTGCGCGTtta  <  2:550659/141‑1 (MQ=255)                                                                                                                                 ccACCGGAGAAAGAGCAAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAGACCCTTGTGGACCATCATGTCCAAATTGATCATAGCTTGCGCGTtta  <  2:668209/141‑1 (MQ=255)                                                                                                                                       |                                                                                                                                       CGCATGTTACATCTTTACGGATTGAAATTTCTTTTGTTGTACCAAATACCGCTTCTTCAAATGTTAATGTCATTGTATACTGAAGATCATCACCTTTTTGCGGTGCATTTGGATCTCTTTGTCTGCCGCCACCGAAGAAAGAGCTAAAGATATCTTCAAAACCGCCGCCACCGAAGCCACTAAAACCGCCAAAGTCAGAGCCATTGAATCCTTGTCCACCAAAACCTTGTGGACCATCATGTCCAAATTGATCATAGCTTGCGCGTTTA  >  CP000730/1689418‑1689686

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑