Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,817,851	T→C	F27S (TTC→TCC)	cho →	excinuclease Cho

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,817,851	0	T	C	76.7%	83.1 / 26.7	43	F27S (TTC→TCC)	cho	excinuclease Cho
Reads supporting (aligned to +/- strand):  ref base T (4/6);  new base C (14/19);  total (18/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.22e-01

TTAATCGCTTCCCGCCTGTTACACTGGATAGATAACCAGCATTCGGAGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATTCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCCGCGTCCTTTCTCATTTACGTACCCCGGATGAAGCCG  >  NZ_CP009273/1817718‑1817985                                                                                                                                      |                                                                                                                                       ttAATCGCTTCCCGCCTGTTACACTGGATAGATAACCAGCATTCGGAGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATTCCtt                                                                                                                                    <  1:58977/138‑1 (MQ=255) ttAATCGCTTCCCGCCTGTTACACTGGATAGATAACCAGCATTCGGAGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCtt                                                                                                                                    <  1:666640/138‑1 (MQ=255)    aTCGCTTCCCGCCTGTTACACTGGATAGATAACCAGCATTCGGAGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAAt                                                                                                                                 >  1:294849/1‑138 (MQ=255)       gCTTCCCGCCTGTTACACTGGATAGATAACCAGCATTCGGAGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATTCCTTAATGACt                                                                                                                             >  2:732492/1‑139 (MQ=255)              gCCTGTTACACTGGATAGATAACCAGCATTCGGAGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTacccac                                                                                                                      <  2:294849/139‑1 (MQ=255)                     acacTGGATAGATAACCAGCATTCGGAGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGAcc                                                                                                                <  2:511238/138‑1 (MQ=255)                                     cAGCATTCGGAGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGAc                                                                                                                 >  2:556180/1‑121 (MQ=255)                                     cAGCATTCGGAGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGAc                                                                                                                 <  1:556180/121‑1 (MQ=255)                                     cAGCATTCGGAGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGttt                                                                                                >  1:810825/1‑138 (MQ=255)                                        cATTCGGAGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATTCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATg                                                                                            <  2:810364/139‑1 (MQ=255)                                        cATTCGGAGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATg                                                                                            >  1:12369/1‑139 (MQ=255)                                          ttCGGAGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGt                                                                                          <  2:810825/139‑1 (MQ=255)                                          ttCGGAGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGt                                                                                          >  1:40154/1‑139 (MQ=255)                                               aGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAg                                                                                     <  1:89936/139‑1 (MQ=255)                                                  cAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGa                                                                                  >  1:748815/1‑139 (MQ=255)                                                       gTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCa                                                                             <  1:866076/139‑1 (MQ=255)                                                          gTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATg                                                                           <  1:598027/138‑1 (MQ=255)                                                          gTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATg                                                                           <  2:40154/138‑1 (MQ=255)                                                             cGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACCTTCATTCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGc                                                                       >  1:140150/1‑139 (MQ=255)                                                              ggCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATTCCTTAATGACTTacccac                                                                                                                      >  2:588484/1‑91 (MQ=255)                                                              ggCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATTCCTTAATGACTTacccac                                                                                                                      <  1:588484/91‑1 (MQ=255)                                                              ggCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGTTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGct                                                                      <  2:62868/139‑1 (MQ=255)                                                                  tttAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATTCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCta                                                                   >  2:330936/1‑138 (MQ=255)                                                                  tttAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCta                                                                   >  1:270701/1‑138 (MQ=255)                                                                    tAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTatat                                                                >  2:861137/1‑139 (MQ=255)                                                                     aaCTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGAc                                                                                                                 >  1:230998/1‑89 (MQ=255)                                                                     aaCTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGAc                                                                                                                 <  2:230998/89‑1 (MQ=255)                                                                          ctcCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCa                                                           >  1:139345/1‑138 (MQ=255)                                                                                            aaGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAg                                        >  2:540686/1‑139 (MQ=255)                                                                                               cTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATTCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCcg                                     <  2:679118/139‑1 (MQ=255)                                                                                                       aTTTATGAATATCCCGAACATTTACGTTCATTCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCCGCGTCCttt                             <  1:732492/139‑1 (MQ=255)                                                                                                       aTTTATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCCGCGTCCttt                             <  2:748815/139‑1 (MQ=255)                                                                                                          tATGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCCGCGTCCTTtct                           <  1:540686/138‑1 (MQ=255)                                                                                                            tGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCCGCGTCCTTTCTCa                         <  2:304382/138‑1 (MQ=255)                                                                                                            tGAATATCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCCGCGTCCTTTCTCa                         <  1:861137/138‑1 (MQ=255)                                                                                                                  tCCCGAACATTTACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCCGCGTCCTTTCTCATTTACg                   >  2:331260/1‑138 (MQ=255)                                                                                                                   cccGAACATTTACGTTCATCCCTTAATGACTTACCCA‑CCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCCGCGTCCTTtct                           >  2:448689/1‑128 (MQ=255)                                                                                                                   cccGAACATTTACGTTCATCCCTTAATGACTTACCCA‑CCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCCGCGTCCTTtct                           <  1:448689/128‑1 (MQ=255)                                                                                                                            ttACGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCCGCGTCCTTTCTCATTTGCGTACCCCGGAt         >  2:841021/1‑138 (MQ=255)                                                                                                                               ccttCATTCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCCGCGTCCTTTCTCATTTACGTACCCCGGATGAAg     <  2:140150/137‑1 (MQ=255)                                                                                                                               cGTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCCGCGTCCTTTCTCATTTACGTACCCCGGATGAAg     <  2:12369/139‑1 (MQ=255)                                                                                                                                gTTCATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCCGCGTCCTTTCTCATTTACGTACCCCGGATGAAgc    <  2:139345/139‑1 (MQ=255)                                                                                                                                   cATCCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCCGCGTCCTTTCTCATTTACGTACCCCGGATGAAgccg  <  2:270701/138‑1 (MQ=255)                                                                                                                                      |                                                                                                                                       TTAATCGCTTCCCGCCTGTTACACTGGATAGATAACCAGCATTCGGAGTCAACAGTGGTACGGCGTTTAACTTCTCCGCGGCTCGAATTTGAAGCTGCGGCAATTTATGAATATCCCGAACATTTACGTTCATTCCTTAATGACTTACCCACCCGACCAGGGGTGTATCTGTTTCATGGTGAAAGTGACACCATGCCGCTCTATATCGGCAAAAGCGTTAACATCCGCAGCCGCGTCCTTTCTCATTTACGTACCCCGGATGAAGCCG  >  NZ_CP009273/1817718‑1817985

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑