Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,352,815	G→A	100%	A92V (GCA→GTA)	rpsI ←	ribosomal protein S9

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,352,815	0	G	A	100.0%	173.2 / NA	58	A92V (GCA→GTA)	rpsI	ribosomal protein S9
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (32/26);  total (32/26)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TATCGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTAAAATT  >  CP000730/2352678‑2352952                                                                                                                                          |                                                                                                                                          tatCATCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACtt                                                                                                                                        >  1:408259/1‑141 (MQ=255)       ccGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaata                                                                                                                                  >  2:119197/1‑141 (MQ=255)         gACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGATCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTaataat                                                                                                                                >  2:87943/1‑141 (MQ=255)           cAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGGTCTACTTCTAATGATGc                                                                                                                              >  2:318914/1‑141 (MQ=255)            aaTTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCCGGATCTACTTCTAATAATGcc                                                                                                                             >  1:491758/1‑140 (MQ=255)               tAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGGTCTACTTCTAATAATGCACGa                                                                                                                          >  1:499731/1‑141 (MQ=255)                taCGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAg                                                                                                                         <  1:373313/140‑1 (MQ=255)                 aCGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGGTCTACTTCTAATAATGCACGAGc                                                                                                                        >  1:6685/1‑141 (MQ=255)                    ttttGAGAATTGAGGTGAACGACGAGTTGCTTTAAGACCTGGTTTATTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGAt                                                                                                                     <  1:130446/141‑1 (MQ=255)                                   tGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagc                                                                                                      <  2:125000/141‑1 (MQ=255)                                   ggAACGACAAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagc                                                                                                      <  2:11596/140‑1 (MQ=255)                                         acgaGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagc                                                                                                <  1:146397/141‑1 (MQ=255)                                              ctgctTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCTGGATCTACTTCTAGTAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTc                                                                                           >  1:157131/1‑141 (MQ=255)                                                    taaaaaccgattttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGa                                                                                     <  1:152956/131‑1 (MQ=255)                                                         ccTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAacca                                                                                <  1:222910/141‑1 (MQ=255)                                                          cTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCGGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccac                                                                               >  1:146795/1‑141 (MQ=255)                                                             gTTTTTTTCGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccaccac                                                                            <  2:98878/141‑1 (MQ=255)                                                             gTTTTTTACTTTTTTTCATACGTGGAAAACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTTACTTATAGCTTGAGCTTGTCCAGTGAAaccaccac                                                                            >  2:511694/1‑141 (MQ=255)                                                             gTTTTTTACGTTCTTGCATACGTGGGTCACGAGGAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccaccac                                                                            <  1:178416/141‑1 (MQ=255)                                                                   tACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGGTTGTCGAGTGAAACCACCACCCTGaa                                                                      >  1:321034/1‑141 (MQ=255)                                                                    aCGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTACAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCAATTCCGTGACGGATAGCTTGTGCTTGTCCAGAGACACCACCACCACGaaa                                                                     >  2:373181/1‑140 (MQ=255)                                                                      gTTCTTTCATCCGTGGGCCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATCCAGGAGCTACTTCCAATAATGCACGAGCGATTCCGTGACGGATAGCTCGACCTTGTCCAGTGCACCCCACACCCTGAACGt                                                                   >  2:127109/1‑141 (MQ=255)                                                                      gTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGACCCTCTGTATTCAGGCTCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGacgct                                                                   >  2:18243/1‑137 (MQ=255)                                                                      gTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGGTCTACTTCTACTAATGCACGGGCGATTCCGTGGCGGATTACTTGAGGTTGTCCAGTGAAACCCCCACCATGAACGt                                                                   >  2:324013/1‑141 (MQ=255)                                                                       ttCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCAACAtcctcgtt                                                                  <  2:493199/141‑8 (MQ=255)                                                                           ttCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACt                                                              >  1:29299/1‑141 (MQ=255)                                                                             cATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTaa                                                            <  2:464191/141‑1 (MQ=255)                                                                              aTACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCCCCACCATGAACGTTAACTaaa                                                           >  2:71381/1‑141 (MQ=255)                                                                               tACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCCTGAACGTTAACTaaaa                                                          >  2:152930/1‑141 (MQ=255)                                                                                aCGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTGGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAc                                                         >  2:55197/1‑141 (MQ=255)                                                                                   tGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcatc                                                      >  1:224182/1‑141 (MQ=255)                                                                                          cGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATCGCTTGAGCTTGTCCAGTGAAACCACCCCCATGAACGTTAACTAAAACATCATAGTTa                                               >  2:174049/1‑141 (MQ=255)                                                                                              taagtaaTCCAGCGCGTTTTAAACAACCTCTGTATTCAAGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATTAACGTTAACTAAAACATCATAGTTACCtt                                           <  1:64809/141‑1 (MQ=255)                                                                                                agtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTACCTAAAACATCATAGTTACCTTTa                                         >  1:125712/1‑141 (MQ=255)                                                                                                agtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATCGTTACCTTTa                                         >  1:232840/1‑141 (MQ=255)                                                                                                  taaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGt                                       <  1:100293/141‑1 (MQ=255)                                                                                                  taaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCAAGAGCGATTCCGTGACGGATAGATTGAGCTTGTACAGTCAAACGACCACCATGAACGTTAACTAAAACATCATAGTTACATCTAGt                                       >  2:545404/1‑141 (MQ=255)                                                                                                       caacgcgTTTTAAAGTACCTCTGTAAGCAGAAACTACTTCTAATAATGAACGAGCGATTCCGTGACGGATAGCTTGAGCTTGGCCAGTGAAACCACCACCATGAACGCTAACTAAAACATCATGGTTCCCGTTCGTCTCAg                                  >  2:431887/4‑141 (MQ=255)                                                                                                       cAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAg                                  >  2:527195/1‑141 (MQ=255)                                                                                                         gcgcGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGtt                                >  2:305979/1‑141 (MQ=255)                                                                                                              ttttAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATc                           <  1:232091/141‑1 (MQ=255)                                                                                                              ttttAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATc                           <  1:231846/141‑1 (MQ=255)                                                                                                              ttttAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATc                           <  1:119197/141‑1 (MQ=255)                                                                                                              ttttAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATc                           >  1:264516/1‑141 (MQ=255)                                                                                                              ttttAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATc                           >  1:264698/1‑141 (MQ=255)                                                                                                               tttAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCa                          >  1:92652/1‑141 (MQ=255)                                                                                                               tttAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCa                          >  1:519900/1‑141 (MQ=255)                                                                                                                ttAAATAATCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCaa                         <  2:108643/141‑1 (MQ=255)                                                                                                                ttAAAGAACCTCTGTATTCAGGATCTACGTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCaa                         <  1:264530/141‑1 (MQ=255)                                                                                                                 tAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCaaa                        <  1:464068/141‑1 (MQ=255)                                                                                                                    aGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACCTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAtgg                     <  2:370180/141‑1 (MQ=255)                                                                                                                      aaCCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAtggtt                   <  1:511484/141‑1 (MQ=255)                                                                                                                        ccTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACTTCATAGTTACCTTTAGTTTCAGTTACATCAAAtggttgg                 <  2:286600/141‑1 (MQ=255)                                                                                                                        ccTCTGCATTCAGGATCCACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATAATAGTTACCTTTAGTTTCAGTTACATCAAAtggttgg                 <  2:74641/141‑1 (MQ=255)                                                                                                                                ttCAGGCTCTACTTCTAATAATGCACGAGCAATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTc         <  2:479168/141‑1 (MQ=255)                                                                                                                                ttCAGGATCGATTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGATCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTc         <  2:187114/141‑1 (MQ=255)                                                                                                                                  cAGGATCTACTTCTAACAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATTAGATGGTTGGTTTAGGTCTa       >  1:284382/1‑141 (MQ=255)                                                                                                                                       tCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTAAAAtt  <  2:433878/141‑1 (MQ=255)                                                                                                                                          |                                                                                                                                          TATCGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTAAAATT  >  CP000730/2352678‑2352952

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: ‑