Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,534,634	T→A	7.4%	intergenic (+72/‑48)	cpo → / → PP_4022	non‑heme chloroperoxidase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,534,634	0	T	A	7.4%	157.2 / 2.3	54	intergenic (+72/‑48)	cpo/PP_4022	non‑heme chloroperoxidase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (26/24);  new base A (2/2);  total (28/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01

CCCGCATGGCATGCCCACCACCCATGCCGATGTGATCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACAGCCATGCTCACATTCAAACAAACACCTGACTCAGCCGC  >  NC_002947/4534493‑4534776                                                                                                                                              |                                                                                                                                                cccGCTTGGCATTGCCACCCCCCATGGCGTTTTTATCAATGGTGATTTGCTCGCCTTCATCCAAAGCTTATGTGAACGCCTGGACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTtggtgg                                                                                                                                            <  6:267650/147‑1 (MQ=255) cccGCATGGCATGCCCACCACCCATGCCGATGTGATCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCGCTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTtggtgg                                                                                                                                            <  1:169311/147‑1 (MQ=255) cccGCATGGCAGGCCCACCACCCATGCCGATGTGATCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCt                                                                                                                                          <  2:64657/149‑1 (MQ=255)  ccGCATGGCATGCCCACCACCCATGCCGATGTGATCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCtt                                                                                                                                         >  1:237890/1‑149 (MQ=255)     catggcatgCCCACCACCCATGCCGATGTGATCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTtgca                                                                                                                                      <  1:11701/149‑1 (MQ=255)     catggcatgCCCACCACCCATGCCGATGTGATCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTtgca                                                                                                                                      <  5:159433/149‑1 (MQ=255)            tgCCCACCACCCATGCCGATGTGATCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTtg                                                                                                                                        >  7:107477/1‑140 (MQ=255)            tgCCCACCACCCATGCCGATGTGATCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTtg                                                                                                                                        <  8:107477/140‑1 (MQ=255)               ccaccaCCCATGCCGATGTGATCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAg                                                                                                                            >  7:12519/1‑149 (MQ=255)               ccaccaCCCATGCCGATGTGATCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACCAAGTGGCtcatgggg                                                                                                                                   <  4:145659/142‑8 (MQ=255)               ccaccaCCCATGCCGATGTGATCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACCAAGTGGCtcatgggg                                                                                                                                   >  3:145659/1‑135 (MQ=255)                    accCATGCCGATGTGATCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGtt                                                                                                                       <  6:105989/149‑1 (MQ=255)                         tGCCGATGTGATCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGa‑aa                                                                                                                 <  8:134725/149‑1 (MQ=255)                                  gATCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCGTGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCAtt                                                                                                         >  6:189371/1‑148 (MQ=255)                                   aTCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTCTTCAGAGACCCGCTCCCCCATGAGCCACTTGGAGGCTTGCACTGCACTTAGGGGTTAGA‑AACTAGCAatt                                                                                                        >  6:196373/1‑148 (MQ=255)                                      aaTGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCGTGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTAc                                                                                                    <  5:189371/149‑1 (MQ=255)                                                     gCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACCAAGTGGCt                                                                                                                                          <  2:143575/97‑1 (MQ=255)                                                     gCCTTCATCCAAAGATGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACCAAGTGGCt                                                                                                                                          >  1:143575/1‑97 (MQ=255)                                                        ttCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGAGc                                                                                   >  2:161016/1‑148 (MQ=255)                                                               aaaGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATAc                                                                            >  1:178705/1‑148 (MQ=255)                                                               aaaGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATAc                                                                            >  8:26528/1‑148 (MQ=255)                                                                 aGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGAGCAAAATACGAt                                                                         <  1:161016/149‑1 (MQ=255)                                                                  gCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTGCTGTTGAGAGACCCGCGCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAATTACGATg                                                                        <  5:196373/149‑1 (MQ=255)                                                                   cTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATga                                                                       <  2:237890/149‑1 (MQ=255)                                                                     gATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGAt                                                                         >  5:162238/1‑145 (MQ=255)                                                                      aTGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATgaga                                                                     <  8:12519/148‑1 (MQ=255)                                                                                cTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCgg                                                                                     >  2:272452/1‑122 (MQ=255)                                                                                   cACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATc                                                       >  6:73068/1‑149 (MQ=255)                                                                                    aCGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGa                                                                          >  4:19340/1‑129 (MQ=255)                                                                                    aCGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGa                                                                          <  3:19340/129‑1 (MQ=255)                                                                                       ggTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGa                                                   <  5:73068/149‑1 (MQ=255)                                                                                          cTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATcc                                                      >  6:222630/1‑143 (MQ=255)                                                                                          cTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATcc                                                      <  5:222630/143‑1 (MQ=255)                                                                                           tttttGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATc                                                       <  4:89735/141‑1 (MQ=255)                                                                                           tttttGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATc                                                       >  3:89735/1‑141 (MQ=255)                                                                                            ttttGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACgtg                                              >  2:93339/1‑149 (MQ=255)                                                                                             tttGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACgt                                               <  1:134062/147‑1 (MQ=255)                                                                                                   gTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTAc                                                                                                    >  8:227807/1‑88 (MQ=255)                                                                                                      aCTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACAGCCa                                    >  4:32946/1‑149 (MQ=255)                                                                                                       cTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGAt                                                                         >  8:188318/1‑111 (MQ=255)                                                                                                       cTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGAt                                                                         <  7:188318/111‑1 (MQ=255)                                                                                                       cTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACAGCCAt                                   >  2:282927/1‑149 (MQ=255)                                                                                                          aGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACAGCCATGc                                 <  1:282927/148‑1 (MQ=255)                                                                                                          aGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACAGCCATGCt                                <  1:93339/149‑1 (MQ=255)                                                                                                           gTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACAGCCATGCTc                               <  7:26528/149‑1 (MQ=255)                                                                                                              cTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACAGCCATGCTcaca                            >  7:175147/1‑149 (MQ=255)                                                                                                              cTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACAGCCATGCTcaca                            >  7:21474/1‑149 (MQ=255)                                                                                                                     gagaCCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACAGCCATGCTCACATTcaaac                     <  8:175147/149‑1 (MQ=255)                                                                                                                          ccGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCAGTCAACTCATCCTGAACGTGTTGACAGCCATGCTCACATTCAaacaaaca                >  6:333571/1‑149 (MQ=255)                                                                                                                          ccGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACAGCCATGCTCACATTCAaacaaaca                >  4:63058/1‑149 (MQ=255)                                                                                                                          ccGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACAGCCATGCTCACATTCAaacaaaca                >  2:66073/1‑149 (MQ=255)                                                                                                                                ccccATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACAGCCATGCTCACATTCAAACAAACACCTGa           <  6:121378/148‑1 (MQ=255)                                                                                                                                ccccATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACAGCCATGCTCACATTCAAACAAACACCTGa           <  3:63058/148‑1 (MQ=255)                                                                                                                                 cccATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACa                                        >  4:32140/1‑118 (MQ=255)                                                                                                                                 cccATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACa                                        <  3:32140/118‑1 (MQ=255)                                                                                                                                         ccACTTGGTGGCTTGCACTGCACTTAGGGGTTTGATAACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACAGCCATGCTCACATTCAAAAAAACACCTGACTCAgccgc  >  1:211130/1‑149 (MQ=255)                                                                                                                                              |                                                                                                                                                CCCGCATGGCATGCCCACCACCCATGCCGATGTGATCAATGCGGATTTGCTCGCCTTCATCCAAAGCTGATGTGAACGCCTGCACGGGTCTTTTTGCAGTCACTAAGTCCTGTTGAGAGACCCGCTCCCCCATGAGCCACTTGGTGGCTTGCACTGCACTTAGGGGTTTGA‑AACTAGCATTTCTACCAGTTGCTCATCCGGGCAAAATACGATGAGATCACTCAACTCATCCTGAACGTGTTGACAGCCATGCTCACATTCAAACAAACACCTGACTCAGCCGC  >  NC_002947/4534493‑4534776

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑