Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP002094	2,183,875	(A)5→4	coding (399/1161 nt)	LLNZ_11440 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP002094	2,183,871	0	A	.	100.0%	346.6 / NA	72	coding (403/1161 nt)	LLNZ_11440	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (35/37);  total (35/37)

ATTTCTGCTTCCGCAAACTCTTCTCTTAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAGAAAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCACTTTCAAATAGCTTCAAACG  >  CP002094/2183774‑2183964                                                                                                  |                                                                                              aTTTCTGCTTCCGCAAACTCTTCTCTTAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAGaa                                                                                              >  2:468857/1‑99 (MQ=255) aTTTCTGCTTCCGCAAACTCTTCTCTTAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAGaa                                                                                              <  2:1387749/99‑1 (MQ=255)    tCTGCTTCCGCAAACTCTTCTCTTAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAGaaaat                                                                                           <  2:1111879/99‑2 (MQ=255)      tGCTTCCGCAAACTCTTCTCTTAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAGaaaatcc                                                                                         <  2:1069647/99‑4 (MQ=255)        cTTCCGCAAACTCTTCTCTTAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTg                                                                                      <  1:310914/99‑1 (MQ=255)        cTTCCGCAAACTCTTCTCTTAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTg                                                                                      >  1:87028/1‑99 (MQ=255)           ccGCAAACTCTTCTCTTAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTc                                                                                   <  1:1031365/99‑1 (MQ=255)              cAAACTCTTCTCTTAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCgg                                                                                >  2:1396861/1‑99 (MQ=255)                      tctcttAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGaa                                                                              >  2:271092/1‑93 (MQ=255)                      tctcttAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGaa                                                                              <  1:271092/93‑1 (MQ=255)                      tctcttAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCa                                                                        >  2:376303/1‑99 (MQ=255)                      tctcttAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCa                                                                        <  1:58678/99‑1 (MQ=255)                       ctcttAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCAt                                                                       >  2:720873/1‑99 (MQ=255)                          ttAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATTTGCATGAg                                                                    <  2:1011199/99‑1 (MQ=255)                           tAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGt                                                                   <  1:1151644/99‑1 (MQ=255)                              cTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCa                                                                >  1:961806/1‑99 (MQ=255)                                gTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAg                                                              <  2:1067147/99‑1 (MQ=255)                                  aTCTTATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCa                                                            >  1:21839/1‑99 (MQ=255)                                  aTCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCa                                                            <  1:867933/99‑1 (MQ=255)                                  aTCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCa                                                            >  1:21840/1‑99 (MQ=255)                                   tCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCAt                                                           >  2:1313400/1‑99 (MQ=255)                                   tCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCAt                                                           <  1:1422261/99‑1 (MQ=255)                                    cATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCAtt                                                          <  1:133771/99‑1 (MQ=255)                                     atatCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTg                                                         <  1:1561262/99‑1 (MQ=255)                                       atCCAACCAGTTGATATAATGAACAAAATAATCTTCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCa                                                       <  1:781193/99‑1 (MQ=255)                                       atCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCa                                                       <  1:739730/99‑1 (MQ=255)                                       atCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCAGTTCCGGAATGTGCATGAGTCCAAGCATTGCa                                                       >  1:345650/1‑99 (MQ=255)                                        tCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCat                                                      >  1:821918/1‑99 (MQ=255)                                        tCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCat                                                      >  2:1145622/1‑99 (MQ=255)                                           aaCCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCatcaa                                                   <  2:726716/99‑1 (MQ=255)                                            aCCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCatcaat                                                  >  2:1468832/1‑99 (MQ=255)                                               aGTTGATATAATTAACAAAATAATCATCCTTACTTTCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATgac                                               >  2:910946/1‑99 (MQ=255)                                                gTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATcaca                                              <  1:663938/99‑1 (MQ=255)                                                 ttGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCAcat                                             >  1:604546/1‑99 (MQ=255)                                                 ttGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCAcat                                             <  1:183005/99‑1 (MQ=255)                                                   gATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCAcatca                                           >  1:1569718/1‑99 (MQ=255)                                                    atatAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCAcatcat                                          <  1:1193883/99‑1 (MQ=255)                                                    atatAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCAcatcat                                          <  1:375565/99‑1 (MQ=255)                                                     tataATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATa                                         <  2:250851/99‑1 (MQ=255)                                                      ataATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATaa                                        <  1:214872/99‑1 (MQ=255)                                                        aaTGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAgg                                      <  2:767025/99‑1 (MQ=255)                                                        aaTGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAgg                                      <  2:382013/99‑1 (MQ=255)                                                        aaTGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAgg                                      <  2:1514426/99‑1 (MQ=255)                                                         aTGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGt                                     >  2:1204802/1‑99 (MQ=255)                                                         aTGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGt                                     >  1:1233286/1‑99 (MQ=255)                                                          tGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTa                                    <  1:1025975/99‑1 (MQ=255)                                                          tGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTa                                    <  2:1545605/99‑1 (MQ=255)                                                          tGAACAAAATAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTa                                    >  1:1260280/1‑99 (MQ=255)                                                               aaaaTAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCaaa                               <  1:1205043/99‑1 (MQ=255)                                                               aaaaTAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCaaa                               <  2:1193518/99‑1 (MQ=255)                                                                aaaTAATCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCaaaa                              <  2:730885/99‑1 (MQ=255)                                                                 aataatCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAAt                             >  1:8928/1‑99 (MQ=255)                                                                 aataatCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAAt                             <  2:538573/99‑1 (MQ=255)                                                                 aataatCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAAt                             <  1:887708/99‑1 (MQ=255)                                                                   taatCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAAttt                           >  2:966100/1‑99 (MQ=255)                                                                   taatCATCCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGACCAAGCATTGCATCAATCACATCATAAGGTATCAAAAttt                           >  1:1565678/1‑99 (MQ=255)                                                                     atcatcCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAAttttt                         >  2:490098/1‑99 (MQ=255)                                                                       catcCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTcc                       >  1:481688/1‑99 (MQ=255)                                                                        atcCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCa                      <  2:1179772/99‑1 (MQ=255)                                                                         tccttcctTCCATTGATCATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCTCATCATAAGGTAGCAAAATTTTTCCAc                     <  1:298415/99‑1 (MQ=255)                                                                         tcCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCAc                     <  1:500046/99‑1 (MQ=255)                                                                         tcCTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCAc                     <  1:749802/99‑1 (MQ=255)                                                                          ccTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCACt                    <  2:1390085/99‑1 (MQ=255)                                                                          ccTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCACt                    <  1:1597322/99‑1 (MQ=255)                                                                          ccTTACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCACt                    <  1:1645400/99‑1 (MQ=255)                                                                            ttACTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCACttt                  >  2:1463983/1‑99 (MQ=255)                                                                               cTTCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCGAAATTTTTCCACTTTCaa               >  1:396357/1‑99 (MQ=255)                                                                                ttCCATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCACTTTCaaa              >  1:478191/1‑99 (MQ=255)                                                                                  ccATTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCACTTTCAAATa            >  2:778651/1‑99 (MQ=255)                                                                                    aTTGATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTGTTCCACTTTCAAATAGc          >  1:339231/1‑99 (MQ=255)                                                                                       gATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCACTTTCAAATAGCTTc       >  2:442411/1‑99 (MQ=255)                                                                                       gATAATATAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCACTTTCAAATAGCTTc       >  1:553255/1‑99 (MQ=255)                                                                                           atatAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCACTTTCAAATAGCTTCAAAc   >  2:399476/1‑99 (MQ=255)                                                                                           atatAAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCACTTTCAAATAGCTTCAAAc   >  1:1158112/1‑99 (MQ=255)                                                                                            tataAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCACTTTCAAATAGCTTCAAACg  >  1:1068808/1‑99 (MQ=255)                                                                                            tataAG‑AAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCACTTTCAAATAGCTTCAAACg  >  2:1265799/1‑99 (MQ=255)                                                                                                  |                                                                                              ATTTCTGCTTCCGCAAACTCTTCTCTTAACTGTATCATATCCAACCAGTTGATATAATGAACAAAATAATCATCCTTACTTCCATTGATAATATAAGAAAAATCCTGTTCCGGAATGTGCATGAGTCCAAGCATTGCATCAATCACATCATAAGGTAGCAAAATTTTTCCACTTTCAAATAGCTTCAAACG  >  CP002094/2183774‑2183964

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑