Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,047,923	(T)5→4	coding (896/1074 nt)	yccM ←	4Fe‑4S binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,047,919	0	T	.	98.0%	217.9 / ‑2.0	51	coding (900/1074 nt)	yccM	4Fe‑4S binding protein
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base . (27/23);  total (27/24)
Fisher's exact test for biased strand distribution p-value = 4.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.76e-01

CGGTACAATTCCTCCGGCACCGGGCTTTGCCATACTCCCGCATACATTGCGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGGTTTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGAATTAATTTATCGACCGGGATCCGTGATGGGCAATTTTTTGCG  >  NZ_CP009273/1047782‑1048048                                                                                                                                          |                                                                                                                                  cGGTACAATTCCTCCGGCACCGGGCTTTGCCATACTCCCGCATACATTGCGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGGtt                                                                                                                                  >  2:475313/1‑139 (MQ=255)                ggCACCGGGCTTTGCCATACTCCCGCATACATTGCGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGt                                                                                                                  <  1:475313/139‑1 (MQ=255)                            tGCCATACTCCCGCATACATTGCGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAgg                                                                                                       <  2:234773/138‑1 (MQ=255)                                        gCATACATTGCGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGa                                                                                          >  1:7652/1‑139 (MQ=255)                                           tACATTGCGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGActc                                                                                       >  1:88161/1‑139 (MQ=255)                                              aTTGCGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGt                                                                                                                  >  2:795715/1‑109 (MQ=255)                                              aTTGCGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGt                                                                                                                  <  1:795715/109‑1 (MQ=255)                                              aTTGCGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTAc                                                                                    >  2:537445/1‑139 (MQ=255)                                              aTTGCGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTAc                                                                                    >  2:436360/1‑139 (MQ=255)                                                tGCGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTAc                                                                                                   >  2:620321/1‑122 (MQ=255)                                                tGCGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTAc                                                                                                   <  1:620321/122‑1 (MQ=255)                                                 gCGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGc                                                                                  <  2:87779/138‑1 (MQ=255)                                                 gCGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGc                                                                                  <  1:1164410/138‑1 (MQ=255)                                                  cGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGc                                                                                  >  1:311732/1‑137 (MQ=255)                                                  cGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGc                                                                                  >  1:878734/1‑137 (MQ=255)                                                   gTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAg                                                                               >  1:414490/1‑139 (MQ=255)                                                      aCCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACa                                                                                             <  2:171516/122‑1 (MQ=255)                                                      aCCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACa                                                                                             >  1:171516/1‑122 (MQ=255)                                                       ccAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCAt                                                                           <  2:1287984/139‑1 (MQ=255)                                                       ccAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCAt                                                                           <  1:977757/139‑1 (MQ=255)                                                          aTCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATa                                                                          >  1:1055844/1‑137 (MQ=255)                                                          aTCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATa                                                                          >  1:369363/1‑137 (MQ=255)                                                                 cAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTa                                                                 >  1:1126376/1‑139 (MQ=255)                                                                        aaTCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATAGCTCTACGCAAGTCATACAGCCGGTACATTCCa                                                          <  2:797828/139‑1 (MQ=255)                                                                         aTCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTa                                                                                                    <  1:1112546/96‑1 (MQ=255)                                                                         aTCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTa                                                                                                    >  2:1112546/1‑96 (MQ=255)                                                                         aTCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCa                                                          <  2:1126376/138‑1 (MQ=255)                                                                         aTCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCa                                                          <  1:953174/138‑1 (MQ=255)                                                                         aTCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCa                                                          <  2:626295/138‑1 (MQ=255)                                                                         aTCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCAc                                                         >  2:534742/1‑139 (MQ=255)                                                                              cAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTc                                                    >  2:489837/1‑139 (MQ=255)                                                                                      gTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTGCCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTg                                             >  1:1014128/1‑138 (MQ=255)                                                                                      gTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACa                                                                                             <  1:18632/90‑1 (MQ=255)                                                                                      gTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACa                                                                                             >  2:18632/1‑90 (MQ=255)                                                                                      gTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTg                                             >  2:1086156/1‑138 (MQ=255)                                                                                      gTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTg                                             >  1:643842/1‑138 (MQ=255)                                                                                              aTTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGt                                                                  <  2:1017158/109‑1 (MQ=255)                                                                                              aTTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGt                                                                  >  1:1017158/1‑109 (MQ=255)                                                                                              aTTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGaattaatt                                     >  2:153901/1‑138 (MQ=255)                                                                                                 aaCCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGAATTAATTTAt                                  <  1:17463/138‑1 (MQ=255)                                                                                                    cagccagACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGAATTAATTTATCGAc                              <  1:1086156/139‑1 (MQ=255)                                                                                                    cagccagACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGAATTAATTTATCGAc                              <  1:903318/139‑1 (MQ=255)                                                                                                     agccagACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGAATTAATTTATCGAcc                             <  2:7652/139‑1 (MQ=255)                                                                                                     agccagACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGAATTAATTTATCGAcc                             <  1:534742/139‑1 (MQ=255)                                                                                                      gccagACAACGCAAAGGCTTTTTTATTTGCCGCAGGTTTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGAATTAATTTATCGAcc                             <  2:252521/139‑1 (MQ=255)                                                                                                      gccagACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGAATTAATTTATCGACCg                            >  2:446092/1‑139 (MQ=255)                                                                                                      gccagACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGAATTAATTTATCGACCg                            <  2:414490/139‑1 (MQ=255)                                                                                                       ccagACAACGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGAATTAATTTATCGACCgg                           >  2:418766/1‑139 (MQ=255)                                                                                                               cGCAAAGGCTTTTTTATTTGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGAATTAATTTATCGACCGGGATCCGt                    >  1:399145/1‑138 (MQ=255)                                                                                                                                ttGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGAATTAATTTATCGACCGGGATCCGTGATGGGCAATTTTTTgcg  >  1:836704/1‑139 (MQ=255)                                                                                                                                 tGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGAATTAATTTATCGACCgg                           <  1:1236207/113‑1 (MQ=255)                                                                                                                                 tGCCGCAGG‑TTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGAATTAATTTATCGACCgg                           >  2:1236207/1‑113 (MQ=255)                                                                                                                                          |                                                                                                                                  CGGTACAATTCCTCCGGCACCGGGCTTTGCCATACTCCCGCATACATTGCGTAACCAATCACCGCAAACATAATCCCCAGAACCAGTAGCGTCATTAACCAGCCAGACAACGCAAAGGCTTTTTTATTTGCCGCAGGTTTTTGCAGTGAAAAGGTCAATGTTGAGGCTACCGGACATGACTCTACGCAAGTCATACAGCCGGTACATTCCACTGTTCGTACCTGAATTAATTTATCGACCGGGATCCGTGATGGGCAATTTTTTGCG  >  NZ_CP009273/1047782‑1048048

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑