Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,405,320	T→C	10.5%	M81V (ATG→GTG)	PP_3886 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,405,320	0	T	C	10.5%	147.9 / 7.9	57	M81V (ATG→GTG)	PP_3886	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (24/27);  new base C (4/2);  total (28/29)
Fisher's exact test for biased strand distribution p-value = 4.23e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01

CCGATAGCCAGCGAACTGCCTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGCCCAGCTGGGTGG  >  NC_002947/4405172‑4405466                                                                                                                                                     |                                                                                                                                                   ccGATAGCCAGCGAACTGCCTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCAt                                                                                                                                                    <  4:215054/149‑1 (MQ=255)        ccAGCGAACTGCCTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGa                                                                                                                                             <  1:103769/149‑1 (MQ=255)         cAGCGAACTGCCTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCTCGGCACATGCCggg                                                                                                                                            >  4:308331/1‑147 (MQ=255)         cAGCGAACTGCCTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGGGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCCTCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAg                                                                                                                                            <  8:234611/149‑1 (MQ=255)          aGCGAACTGCCTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGAATGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAgg                                                                                                                                           >  7:146653/1‑149 (MQ=255)                cTGCCTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGa                                                                                                                                     <  2:192895/149‑1 (MQ=255)                   ccTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCTCGGCACATGCCGGGGCtttttcgt                                                                                                                                  <  3:308331/149‑7 (MQ=255)                       ggAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATggg                                                                                                                                <  7:143215/147‑1 (MQ=255)                       ggAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTg                                                                                                                              <  2:277844/149‑1 (MQ=255)                          aCAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTg                                                                                                                              >  1:5440/1‑146 (MQ=255)                              ggCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATgg                                                                                                                       >  3:373375/1‑149 (MQ=255)                               gCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATgg                                                                                                                       >  8:307786/1‑148 (MQ=255)                                   cccGAGTTCCGCCGATGACCCGTGACTGAATTTGGAGGGACTGGGCAGAAATCTGAGAATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAAcc                                                                                                                  <  3:290127/149‑1 (MQ=255)                                    ccGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAAccc                                                                                                                 >  3:290521/1‑149 (MQ=255)                                     cGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCt                                                                                                                >  4:229/1‑149 (MQ=255)                                         ttCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCa                                                                                                            <  7:307786/149‑1 (MQ=255)                                                gATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCt                                                                                                     <  5:339629/149‑1 (MQ=255)                                                     cccGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGt                                                                                                <  3:229/149‑1 (MQ=255)                                                      ccGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTg                                                                                               >  5:291620/1‑149 (MQ=255)                                                          gACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGgcgc                                                                                           >  8:337222/1‑149 (MQ=255)                                                            cGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCtt                                                                                         <  4:139352/149‑1 (MQ=255)                                                             ggAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTc                                                                                        >  7:129050/1‑149 (MQ=255)                                                             ggAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTc                                                                                        >  2:308153/1‑149 (MQ=255)                                                                       gggACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTcc                                                                              <  7:337222/149‑1 (MQ=255)                                                                              ggCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCt                                                                       <  8:9949/149‑1 (MQ=255)                                                                                  gAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACt                                                                   <  1:308153/149‑1 (MQ=255)                                                                                     aTCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGtt                                                                <  8:129050/149‑1 (MQ=255)                                                                                      tCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTg                                                                                               >  4:287341/1‑117 (MQ=255)                                                                                      tCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTg                                                                                               <  3:287341/117‑1 (MQ=255)                                                                                         gAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTAccc                                                            >  3:106725/1‑149 (MQ=255)                                                                                          aGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTAccc                                                            <  4:373375/148‑1 (MQ=255)                                                                                          aGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTAccc                                                            <  2:5440/148‑1 (MQ=255)                                                                                               cTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCTGCATGAGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTGCCCACGCTGACTGTTACCCCTGCAc                                                      <  8:146653/149‑1 (MQ=255)                                                                                                 aaCGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGt                                                    >  2:287713/1‑149 (MQ=255)                                                                                                          aCGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCgg                                           >  6:246037/1‑149 (MQ=255)                                                                                                          aCGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCgg                                           <  4:106725/149‑1 (MQ=255)                                                                                                              tATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCtt                                       >  4:70529/1‑149 (MQ=255)                                                                                                              tATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCtt                                       >  6:237044/1‑149 (MQ=255)                                                                                                                  cATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTg                                                                                                                              <  8:217193/58‑1 (MQ=255)                                                                                                                  cATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTg                                                                                                                              >  7:217193/1‑58 (MQ=255)                                                                                                                  cATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGat                                   <  4:290521/149‑1 (MQ=255)                                                                                                                       cTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGTGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGatcatc                               <  4:317866/148‑1 (MQ=255)                                                                                                                       cTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCAtct                              >  6:234000/1‑149 (MQ=255)                                                                                                                          gCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCAtctc                             <  8:108245/147‑1 (MQ=255)                                                                                                                          gCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTcc                            <  7:224411/148‑1 (MQ=255)                                                                                                                              cATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCaaaaa                       >  4:263917/1‑149 (MQ=255)                                                                                                                               aTTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAAc                      >  8:10887/1‑149 (MQ=255)                                                                                                                               aTTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAAc                      >  1:231500/1‑149 (MQ=255)                                                                                                                                 ttAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGa                    >  7:290657/1‑149 (MQ=255)                                                                                                                                       aaaaaGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGc              <  8:290657/149‑1 (MQ=255)                                                                                                                                            gCCTCGGCACATGCCGGGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTa                                                               >  4:85710/1‑95 (MQ=255)                                                                                                                                            gCCTCGGCACATGCCGGGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTa                                                               <  3:85710/95‑1 (MQ=255)                                                                                                                                            gCCTCGGCACATGCCGGGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGCCCAGc         >  4:389270/1‑149 (MQ=255)                                                                                                                                            gCCTCGGCACATGCCGGGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGCCCAGc         >  3:361050/1‑149 (MQ=255)                                                                                                                                               ccGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTTCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGCCCAGCTgg      >  6:117111/1‑149 (MQ=255)                                                                                                                                               ccGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGCCCAGCTgg      <  1:287713/149‑1 (MQ=255)                                                                                                                                                cGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGCCCAGCTggg     >  8:310871/1‑149 (MQ=255)                                                                                                                                                   cATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGCCCAGCTGGGTgg  <  5:246037/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                   CCGATAGCCAGCGAACTGCCTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGGTGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGCCCAGCTGGGTGG  >  NC_002947/4405172‑4405466

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑