Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,070,975	G→A	L1122F (CTC→TTC)	putA ←	trifunctional transcriptional regulator/proline dehydrogenase/L‑glutamate gamma‑semialdehyde dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,070,975	0	G	A	92.7%	173.5 / 2.4	55	L1122F (CTC→TTC)	putA	trifunctional transcriptional regulator/proline dehydrogenase/L‑glutamate gamma‑semialdehyde dehydrogenase
Reads supporting (aligned to +/- strand):  ref base G (1/3);  new base A (24/27);  total (25/30)
Fisher's exact test for biased strand distribution p-value = 6.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.70e-01

CTCGCCATATTGCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAGCGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAACCCTTCGCCGCCGAACGGCTGCACACCAACCACTGCGCCCAC  >  NZ_CP009273/1070844‑1071104                                                                                                                                    |                                                                                                                                  cTCGCCATATTGCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACt                                                                                                                            >  2:782772/1‑139 (MQ=255)        tatTGCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAGCGTCACTGCCAgcg                                                                                                                     <  1:303405/139‑1 (MQ=255)             cGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACtt                                                                                                                >  1:619413/1‑139 (MQ=255)                      cGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGa                                                                                                       >  1:337331/1‑139 (MQ=255)                      cGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGa                                                                                                       >  2:427018/1‑139 (MQ=255)                       gCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGAt                                                                                                      >  1:1264642/1‑139 (MQ=255)                            cAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCCGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCCTCCTGACGCGCGAACGTCACGGCCAGCGCACTTTCCGGGCGATTCggc                                                                                                 >  2:394766/1‑137 (MQ=255)                                 cTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGAtt                                                                                                     >  2:417949/1‑130 (MQ=255)                                 cTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGAtt                                                                                                     <  1:417949/130‑1 (MQ=255)                                 cTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCcagca                                                                                             <  1:1066419/138‑1 (MQ=255)                                     aCGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACgg                                                                                        <  2:957875/139‑1 (MQ=255)                                      cGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGt                                                                                       <  1:116277/139‑1 (MQ=255)                                      cGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGt                                                                                       <  2:675057/139‑1 (MQ=255)                                       gATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTa                                                                                      <  1:169459/139‑1 (MQ=255)                                        aTTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTag                                                                                     <  1:782772/139‑1 (MQ=255)                                         tttGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTa                                                                                      >  1:1201811/1‑137 (MQ=255)                                                   aTTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGCTTCGCCAGCAGACGGTAGAGATAGAGCg                                                                           >  2:200990/1‑138 (MQ=255)                                                   aTTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCg                                                                           >  1:820431/1‑138 (MQ=255)                                                    ttCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGa                                                                         <  1:665549/139‑1 (MQ=255)                                                     tCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTc                                                                                                              <  1:915956/101‑1 (MQ=255)                                                     tCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTc                                                                                                              >  2:915956/1‑101 (MQ=255)                                                               cATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATCCTTTGCATCCTGACGCGCGAACGTCACTGCAAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCg                                                                      <  2:43879/131‑1 (MQ=255)                                                               cATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCg                                                                      >  1:43879/1‑131 (MQ=255)                                                               cATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCAAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCttt                                                              >  1:662260/1‑139 (MQ=255)                                                                     gCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGcc                                                         <  1:731068/138‑1 (MQ=255)                                                                     gCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGcc                                                         <  1:340960/138‑1 (MQ=255)                                                                     gCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGcc                                                         <  2:284263/138‑1 (MQ=255)                                                                     gCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGcc                                                         <  2:992618/138‑1 (MQ=255)                                                                       ggCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGa                                                                                                       >  1:672621/1‑90 (MQ=255)                                                                       ggCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGa                                                                                                       <  2:672621/90‑1 (MQ=255)                                                                       ggCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGAc                                                                                          <  1:1095107/103‑1 (MQ=255)                                                                       ggCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGAc                                                                                          >  2:1095107/1‑103 (MQ=255)                                                                            aGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCg                                                 >  1:87626/1‑139 (MQ=255)                                                                            aGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCg                                                 >  2:1173749/1‑139 (MQ=255)                                                                              tCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGa                                               <  2:438813/139‑1 (MQ=255)                                                                                  tGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAAc                                           >  2:571745/1‑139 (MQ=255)                                                                                                gcgcATCGACCGGATCCTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCTCTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAGCCCTTCGCCGCCGaa                             <  1:394766/139‑1 (MQ=255)                                                                                                 cgcATCGACCGGATACTTTGCATCCTGACGCGCGAGCGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAACCCTTCGCCGCCGaa                             <  2:933644/138‑1 (MQ=255)                                                                                                 cgcATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAACCCTTCGCCGCCGaa                             >  2:1112408/1‑138 (MQ=255)                                                                                                 cgcATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAACCCTTCGCCGCCGaa                             <  1:1112408/138‑1 (MQ=255)                                                                                                 cgcATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAACCCTTCGCCGCCGaa                             <  1:139615/138‑1 (MQ=255)                                                                                                 cgcATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAACCCTTCGCCGCCGaa                             <  1:427018/138‑1 (MQ=255)                                                                                                   cATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAgcg                                                                                                                     >  2:179185/1‑48 (MQ=255)                                                                                                   cATCGACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAgcg                                                                                                                     <  1:179185/48‑1 (MQ=255)                                                                                                       gACCGGATACTTTGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAACCCTTCGCCGCCGAACGGCTGc                      <  2:962424/139‑1 (MQ=255)                                                                                                                   tGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCttt                                                              <  2:354167/87‑1 (MQ=255)                                                                                                                   tGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCttt                                                              >  1:354167/1‑87 (MQ=255)                                                                                                                   tGCATCCTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAACCCTTCGCCGCCGAACGGCTGCACaccaacca            <  2:1264642/137‑1 (MQ=255)                                                                                                                         cTGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAACCCTTCGCCGCCGAACGGCTGCACACCAACCACTGCGcc     <  2:1148825/138‑1 (MQ=255)                                                                                                                          tGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAACCCTTCGccgccg                               >  2:770253/1‑111 (MQ=255)                                                                                                                          tGACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAACCCTTCGccgccg                               <  1:770253/111‑1 (MQ=255)                                                                                                                           gACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAACCCTTCGCCGCCGAACGGCTGCACACCAACCACTGCGCccac  >  2:596139/1‑139 (MQ=255)                                                                                                                           gACGCGCGAACGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAACCCTTCGCCGCCGAACGGCTGCACACCAACCACTGCGCccac  >  1:594099/1‑139 (MQ=255)                                                                                                                                 cgAGCGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGcc                                                         <  2:1084990/78‑1 (MQ=255)                                                                                                                                 cgAGCGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGcc                                                         >  1:1084990/1‑78 (MQ=255)                                                                                                                                    |                                                                                                                                  CTCGCCATATTGCGTACATAACGCCTGCAATTCTGGACGATTTGCTGCCCATTCCCGCAGTGCATTTAGCGGCTGAGTCAATGCGGCTTTCAACTGCGCATCGACCGGATACTTTGCATCCTGACGCGCGAGCGTCACTGCCAGCGCACTTTCCGGGCGATTCGCCAGCAGACGGTAGAGATAGAGCGGACCGCCTGCTTTCGGCCCGGTACCGGACAACCCTTCGCCGCCGAACGGCTGCACACCAACCACTGCGCCCAC  >  NZ_CP009273/1070844‑1071104

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑