Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	671,325	A→T	7.7%	Q127L (CAG→CTG)	PP_0573 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	671,325	0	A	T	7.7%	144.3 / 3.3	52	Q127L (CAG→CTG)	PP_0573	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (18/30);  new base T (2/2);  total (20/32)
Fisher's exact test for biased strand distribution p-value = 6.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.82e-01

CAACCCCGACTGGGCCCCGGCCAACACCCGGCTGGTGCTGCAAAAAGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACGTGGTGCTGGTCGAAGGTTACGTACGTGATTACCACGTGGAAGGC  >  NC_002947/671185‑671470                                                                                                                                             |                                                                                                                                                   cAACCCCGACTGGGCCCCGGCCAACACCCGGCTGGTGCTGCAAAAAGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATaca                                                                                                                                            <  8:324686/149‑1 (MQ=255)  aaCCCCGACTGGGCCCCGGCCAACACCCGGCTGGTGCTGCAAAAAGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATacac                                                                                                                                           <  4:10563/149‑1 (MQ=255)     cccGACTGGGCCCCGGCCAACACCCGGCTGGTGCTGCAAAAAGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACAcc                                                                                                                                          >  7:147258/1‑147 (MQ=255)      ccGACTGGGCCCCGGCCAACACCTGGCTGGTGCTGCAAAAAGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATaca                                                                                                                                            >  5:303529/1‑144 (MQ=255)      ccGACTGGGCCCCGGCCAACACCTGGCTGGTGCTGCAAAAAGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATaca                                                                                                                                            <  6:303529/144‑1 (MQ=255)      ccGACTGGGCCCCGGCCAACACCCGGCTGGTGCTGCAAAAAGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAg                                                                                                                                       >  1:330551/1‑149 (MQ=255)         aCTGGGCCCCGGCCAACACCCGGCTGGTGCTGCAAAAAGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGTATTGCTGCAATTCACCCAacgt                                                                                                                                    <  7:246366/149‑2 (MQ=255)         aCTGGGCCCCGGCCAACACCCGGCTGGTGCTGCAAAAAGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAgcgc                                                                                                                                    <  3:20090/149‑1 (MQ=255)         aCTGGGCCCCGGCCAACACCCGGCTGGAGCTGCAAAAAGTGCGCTTCGAGGGCGCCACGGTGTTCCGCTTGCGCGACCTGCGCGAACACTATCAGCCGCTGATCGCGCGGGAAACAACGTTGGGTTAATTGCAGCAATACAGCCAccgc                                                                                                                                    >  5:84486/1‑149 (MQ=255)              gacccGGCAAACAACAGGCTGGTGCTGCAAAAAGTGCGATTCTATGCCGGCACGTTGTTCCACTTGGGCGACCTGCGCTAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTCTGTGAATTGCAGCAATACACCCATCGCCTGAc                                                                                                                               <  6:84486/147‑1 (MQ=255)                                  ggTGCTGCAAAAAGTGCGCTTCGAGGGCGGCACGGTGGTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAgg                                                                                                          <  8:287545/149‑1 (MQ=255)                                   gTGCTGCAAAAAGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑c                                                                                                                    <  3:214077/138‑1 (MQ=255)                                   gTGCTGCAAAAAGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑c                                                                                                                    >  4:214077/1‑138 (MQ=255)                                   gTGCTGCAAAAAGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAggg                                                                                                         <  8:187919/149‑1 (MQ=255)                                   gTGCTGCAAAAAGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAg                                                                                                           <  1:340277/147‑1 (MQ=255)                                         cAAAAAGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACtt                                                                                                   <  6:251598/149‑1 (MQ=255)                                           aaaaGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGc                                                                                                 >  7:24510/1‑149 (MQ=255)                                            aaaGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAAc                                                                                                                          <  4:279282/124‑1 (MQ=255)                                               gTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTc                                                                                             <  6:30899/149‑1 (MQ=255)                                                  cgcTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAAGGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTa                                                                                          <  1:5200/149‑1 (MQ=255)                                                   gcTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTAt                                                                                         <  3:30431/149‑1 (MQ=255)                                                   gcTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTAt                                                                                         <  1:13081/149‑1 (MQ=255)                                                     ttCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTAt                                                                                         <  6:92451/147‑1 (MQ=255)                                                     ttCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTAt                                                                                         >  5:92451/1‑147 (MQ=255)                                                     ttCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGc                                                                                       >  1:47194/1‑149 (MQ=255)                                                       cGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTACCCGGCAGAAGGGCTACTTGCTGTCGTATGc                                                                                       <  1:201382/148‑1 (MQ=255)                                                        gAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTa                                                                                    >  5:176560/1‑149 (MQ=255)                                                             cggcACGGTGTTCTACCTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGc                                                                               <  1:118701/149‑1 (MQ=255)                                                             cggcACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGc                                                                               <  8:24510/149‑1 (MQ=255)                                                                 aCGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGcctcc                                                                           >  7:261502/1‑149 (MQ=255)                                                                     tgtTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAg                                                                       <  6:176560/149‑1 (MQ=255)                                                                          cccTTGGGCGACCTTCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGAtg                                                                   <  8:243864/148‑1 (MQ=255)                                                                               gggCGACCTGCGCGAACACTATCATCCGCTGATCGGGCGCGAAACCACGTTTGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGc                                                               <  4:286311/147‑1 (MQ=255)                                                                               gggCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGcc                                                              >  6:121722/1‑148 (MQ=255)                                                                                  cGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATg                                                          <  8:147258/149‑1 (MQ=255)                                                                                              acacTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACg                                              >  6:191485/1‑149 (MQ=255)                                                                                                  tATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGTATTGCTGCAAt                                                                                                                                               >  7:39460/1‑49 (MQ=255)                                                                                                  tATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGTATTGCTGCAAt                                                                                                                                               <  8:39460/49‑1 (MQ=255)                                                                                                  tATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACgtggt                                          >  1:246670/1‑149 (MQ=255)                                                                                                  tATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACgtggt                                          >  8:162117/1‑149 (MQ=255)                                                                                                    tCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCGACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACGTGGTGc                                        >  8:14217/1‑149 (MQ=255)                                                                                                    tCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTACCTCCTCAGGATGTGGCCGATGGCAGGGTCGACGTGGTGc                                        >  7:142935/1‑149 (MQ=255)                                                                                                      aGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACGTGGTGCTg                                      >  5:27855/1‑149 (MQ=255)                                                                                                       gCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACGTGGTGCTgg                                     <  2:330551/149‑1 (MQ=255)                                                                                                       gCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACGTGGTGCTgg                                     <  2:47194/149‑1 (MQ=255)                                                                                                         cGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACGTGGTGCTGGTc                                   <  2:246670/149‑1 (MQ=255)                                                                                                            tGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACGTGGTGCTGGTCg                                  >  5:253444/1‑147 (MQ=255)                                                                                                              aTCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACGTGGTGCTGGTCGaa                                <  1:38748/147‑1 (MQ=255)                                                                                                              aTCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACGTGGTGCTGGTCGAAg                               <  7:162117/148‑1 (MQ=255)                                                                                                                  ggCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACGTGGTGCTGGTCGAAGGTtac                          <  4:126283/149‑1 (MQ=255)                                                                                                                                 tGGGTGTATTGCTGCAATTCACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACGTGGTGCTGGTCGAAGGTTACGTACGTGATTACCAc           >  7:53727/1‑149 (MQ=255)                                                                                                                                        aTTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACGTGGTGCTGGTCGAAGGTTACGTACGTGATTACCACGTGGaa     <  6:253444/148‑1 (MQ=255)                                                                                                                                           gcagcaATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACGTGGTGCTGGTCGAAGGTTACGTACGTGATTACCACGTGGAAGGc  >  1:182342/1‑148 (MQ=255)                                                                                                                                             |                                                                                                                                                   CAACCCCGACTGGGCCCCGGCCAACACCCGGCTGGTGCTGCAAAAAGTGCGCTTCGAGGGCGGCACGGTGTTCCCCTTGGGCGACCTGCGCGAACACTATCAGCCGCTGATCGGGCGCGAAACCACGTTGGGTGAATTGCAGCAATACACCCAGCGCCTGACCCAACGCTA‑CCGGCAGAAGGGCTACTTGCTGTCGTATGCCTACCTGCCTCCTCAGGATGTGGCCGATGGCAGGGTCGACGTGGTGCTGGTCGAAGGTTACGTACGTGATTACCACGTGGAAGGC  >  NC_002947/671185‑671470

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: ‑