Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,405,320	T→C	17.4%	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	17.4%	96.0 / 13.5	46	M81V (ATG→GTG)	PP_3886	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (22/16);  new base C (2/6);  total (24/22)
Fisher's exact test for biased strand distribution p-value = 1.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCAGCGAACTGCCTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGCCCAGCTGGGTG  >  NC_002947/4405179‑4405465                                                                                                                                              |                                                                                                                                                   ccAGCGAACTGCCTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCAt                                                                                                                                                    <  1:136496/142‑1 (MQ=255) ccAGCGAACTGCCTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCAt                                                                                                                                                    >  2:136496/1‑142 (MQ=255)      gAACTGCCTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCTCGGCACATGCCGGGGCtt                                                                                                                                        <  4:200553/149‑1 (MQ=255)         cTGCCTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCTCGGCACATGCCGGGGCttttt                                                                                                                                     <  4:2642/149‑4 (MQ=255)         cTGCCTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCTCGGCACATGCCGGGACttttt                                                                                                                                     <  2:330300/149‑4 (MQ=255)            ccTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCTCGGCACATGCCGGGGCtttttc                                                                                                                                    <  5:344953/147‑5 (MQ=255)              tGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCTCGGCACATGCCGGGGc                                                                                                                                          <  5:117412/139‑1 (MQ=255)              tGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCTCGGCACATGCCGGGGc                                                                                                                                          >  6:117412/1‑139 (MQ=255)               gggAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑t                                                                                                                              >  2:74014/1‑149 (MQ=255)                   aCAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑Tg                                                                                                                             >  5:228753/1‑146 (MQ=255)                       ggCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATg                                                                                                                       >  4:71987/1‑148 (MQ=255)                                 gTTCGGGCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTc                                                                                                            <  5:295283/149‑1 (MQ=255)                                            gACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTc                                                                                                 >  5:269825/1‑149 (MQ=255)                                                cGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAgg                                                                                                         >  5:103600/1‑137 (MQ=255)                                                cGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAgg                                                                                                         <  6:103600/137‑1 (MQ=255)                                                  tGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGgcg                                                                                           <  6:269825/149‑1 (MQ=255)                                                       gAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTcc                                                                                      >  7:282421/1‑149 (MQ=255)                                                               cgggACTGGGCCGCAAGCTGACCATCTAACGTCTCGACGCAATCCATGACTGGCTCCCTTTACCGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTc                                                                              <  8:282421/148‑1 (MQ=255)                                                                       ggCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCt                                                                      >  4:246830/1‑149 (MQ=255)                                                                          aGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGAc                                                                   >  5:340685/1‑149 (MQ=255)                                                                          aGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGAc                                                                   >  7:192745/1‑149 (MQ=255)                                                                            aaaTCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGgc                                                                                            >  3:262049/1‑122 (MQ=255)                                                                            aaaTCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGgc                                                                                            <  4:262049/122‑1 (MQ=255)                                                                            aaaTCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTg                                                                 >  2:18023/1‑149 (MQ=255)                                                                                   aGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTAcccc                                                          >  3:311709/1‑149 (MQ=255)                                                                                                tcGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGt                                                                >  8:256759/1‑130 (MQ=255)                                                                                                tcGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGt                                                                <  7:256759/130‑1 (MQ=255)                                                                                                tcGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTgccgc                                             >  3:277311/1‑149 (MQ=255)                                                                                                  ggcGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGccgccg                                           >  4:178738/3‑149 (MQ=255)                                                                                                   aCGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTccc                                                                                     >  4:219236/1‑106 (MQ=255)                                                                                                   aCGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTccc                                                                                     <  3:219236/106‑1 (MQ=255)                                                                                                         tCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCtt                                      <  6:228753/147‑1 (MQ=255)                                                                                                           cATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGat                                  <  4:311709/149‑1 (MQ=255)                                                                                                            aTGACTCGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑GGGAGATCCCAACCCTGTCACGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGatc                                 <  2:150545/149‑1 (MQ=255)                                                                                                                   gCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCAtctc                            <  3:178738/147‑1 (MQ=255)                                                                                                                         tttAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAAc                     >  2:330746/1‑148 (MQ=255)                                                                                                                            ccattccaaGCCTCGGCACATGCCGGGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGAc                  >  2:322479/8‑148 (MQ=255)                                                                                                                              cGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACaaa               <  1:74014/149‑1 (MQ=255)                                                                                                                               gAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAg              >  3:125981/1‑149 (MQ=255)                                                                                                                                aaaaaGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGc             >  6:249379/1‑149 (MQ=255)                                                                                                                                 aaaaGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAAc                     >  8:308366/1‑140 (MQ=255)                                                                                                                                 aaaaGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAAc                     <  7:308366/140‑1 (MQ=255)                                                                                                                                   aaGCCTCGGCACATGCCGGGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGCCCa          <  1:322479/149‑1 (MQ=255)                                                                                                                                    aGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGCCCAg         <  4:277311/149‑1 (MQ=255)                                                                                                                                       cccGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGCCCAGCTg      >  1:279450/1‑149 (MQ=255)                                                                                                                                        ccGGCATGTGCCGAGGCTTGGAATGGGATGGAGATGGCAACCCTGTCAGGTCGCTGTCGTg                                                                                              <  1:43350/61‑1 (MQ=255)                                                                                                                                        ccGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGCCCAGCTgg     <  1:18023/149‑1 (MQ=255)                                                                                                                                           gCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGCCCAGCTGGGTg  >  1:238254/1‑149 (MQ=255)                                                                                                                                              |                                                                                                                                                   CCAGCGAACTGCCTGGGAACAGGGCGACCCGAGTTCCGCCGATGACCCGTGACGGAATTTGGAGGGACTGGGCAGAAATCTGAGCATCTAACGTCTCGACGCTATCCATGACTGGCTCCATTTAACGAAAAAGCCCCGGCATGTGCCGAGGCTTGGAATGGG‑TGGAGATGGCAACCCTGTCAGGTCGCTGTCGTGGCGCTTCCCTCCAGTCCCCACGCTGACTGTTACCCCTGCACGTTGCCGCCGGGCTTTGATCATCTCCAAAAACGACAAAGCCCAGCTGGGTG  >  NC_002947/4405179‑4405465

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: ‑