Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,999,490	T→C	intergenic (‑345/‑134)	ygeV ← / → ygeW	sigma‑54‑dependent Fis family transcriptional regulator/knotted carbamoyltransferase YgeW

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,999,490	0	T	C	94.6%	183.7 / 2.3	56	intergenic (‑345/‑134)	ygeV/ygeW	sigma‑54‑dependent Fis family transcriptional regulator/knotted carbamoyltransferase YgeW
Reads supporting (aligned to +/- strand):  ref base T (1/2);  new base C (29/24);  total (30/26)
Fisher's exact test for biased strand distribution p-value = 5.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.06e-01

CCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGAAATAAACCACTTTGCCTGTCATTCCACTACCGGGACTT  >  NZ_CP009273/2999355‑2999619                                                                                                                                        |                                                                                                                                  ccccTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCtt                                                                                                                                >  1:367124/1‑139 (MQ=255) ccccTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCtt                                                                                                                                >  1:64676/1‑139 (MQ=255)       tATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAg                                                                                                                          >  2:171205/1‑139 (MQ=255)            tATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCcgcg                                                                                                                     >  2:79548/1‑139 (MQ=255)             aTTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCcgcgc                                                                                                                    >  2:379694/1‑139 (MQ=255)                 cTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGa                                                                                                                 <  2:468718/138‑1 (MQ=255)                         tAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTgg                                                                                                        >  2:581074/1‑139 (MQ=255)                          agcagcAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTgg                                                                                                        <  1:270712/138‑1 (MQ=255)                          agcagcAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTgg                                                                                                        >  1:265994/1‑138 (MQ=255)                          agcagcAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTgg                                                                                                        >  2:621709/1‑138 (MQ=255)                          agcagcAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTgg                                                                                                        >  1:77617/1‑138 (MQ=255)                           gcagcaAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGca                                                                                                      <  1:215979/139‑1 (MQ=255)                           gcagcaAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGca                                                                                                      <  1:379694/139‑1 (MQ=255)                           gcagcaAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGca                                                                                                      <  1:454233/139‑1 (MQ=255)                           gcagcaAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGc                                                                                                       <  1:171205/138‑1 (MQ=255)                            cagcaAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGca                                                                                                      >  1:830175/1‑138 (MQ=255)                                 aataaataACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCcgc                                                                                                                      >  2:274436/1‑117 (MQ=255)                                 aataaataACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCcgc                                                                                                                      <  1:274436/117‑1 (MQ=255)                                 aataaataACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTa                                                                                                >  1:768336/1‑139 (MQ=255)                                          cgcgATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTc                                                                                       <  2:680574/139‑1 (MQ=255)                                          cgcgATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTa                                                                                                <  1:554910/130‑1 (MQ=255)                                          cgcgATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTa                                                                                                >  2:554910/1‑130 (MQ=255)                                          cgcgATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTc                                                                                       <  2:535964/139‑1 (MQ=255)                                          cgcgATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTc                                                                                       <  2:384877/139‑1 (MQ=255)                                          cgcgATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTc                                                                                       <  1:503964/139‑1 (MQ=255)                                          cgcgATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTc                                                                                       >  1:384877/1‑139 (MQ=255)                                                                          tACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGca                                                                                                      >  2:32396/1‑92 (MQ=255)                                                                          tACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGca                                                                                                      <  1:32396/92‑1 (MQ=255)                                                                               acaacCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGc                                                    >  2:13916/1‑137 (MQ=255)                                                                               acaacCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAAt                                                             >  2:748305/1‑128 (MQ=255)                                                                               acaacCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTCTTAGTCCCAGGTATAGCTGTGAAAACACCAAt                                                             <  1:748305/128‑1 (MQ=255)                                                                                 aacCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGt                                                <  2:77617/139‑1 (MQ=255)                                                                                   ccAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTca                                              <  2:64676/139‑1 (MQ=255)                                                                                         gCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTg                                         >  2:353595/1‑138 (MQ=255)                                                                                           tGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGaaa                                      >  2:354776/1‑139 (MQ=255)                                                                                             gCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGAAAt                                     >  1:442801/1‑138 (MQ=255)                                                                                               aTCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGAAATaaa                                  <  2:265994/139‑1 (MQ=255)                                                                                                             aaCCCCACACATTATCCGTCAAATTAGTCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGAAATAAACCACTTTGCCTGt                     <  1:13916/138‑1 (MQ=255)                                                                                                             aaCCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGAAATAAACCACTTTGCCTGt                     <  2:830175/138‑1 (MQ=255)                                                                                                             aaCCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGAAATAAACCACTTTGCCTGt                     <  1:507304/138‑1 (MQ=255)                                                                                                             aaCCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGAAATAAACCACTTTGCCTGt                     <  1:79548/138‑1 (MQ=255)                                                                                                              aCCCCACACATTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGAAATAAACCACTTTGCCTGTCa                   >  2:319082/1‑139 (MQ=255)                                                                                                                  cacacaTTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGAAATAAACCACTTTGCCTGTCATTc                >  1:641953/1‑138 (MQ=255)                                                                                                                    cacaTTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGc                                                                                                       >  2:321880/1‑49 (MQ=255)                                                                                                                    cacaTTATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGc                                                                                                       <  1:321880/49‑1 (MQ=255)                                                                                                                         tATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTccc                                                                                     >  2:162472/1‑62 (MQ=255)                                                                                                                         tATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTccc                                                                                     <  1:162472/62‑1 (MQ=255)                                                                                                                         tATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTg                                         >  2:40090/1‑106 (MQ=255)                                                                                                                         tATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTg                                         <  1:40090/106‑1 (MQ=255)                                                                                                                         tATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGAAATAAACCACTTTGCCTGTCATTCCACTAc          >  2:572865/1‑137 (MQ=255)                                                                                                                         tATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGAAATAAACCACTTTGCCTGTCATTCCACTAc          <  1:572865/137‑1 (MQ=255)                                                                                                                         tATCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGAAATAAACCACTTTGCCTGTCATTCCACTACCg        >  2:78702/1‑139 (MQ=255)                                                                                                                          aTCCGTCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGAAATAAACCACTTTGCCTGTCATTCCACTACCgg       >  1:673662/1‑139 (MQ=255)                                                                                                                               tCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTc                                                                                       <  2:228290/54‑1 (MQ=255)                                                                                                                               tCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTc                                                                                       >  1:228290/1‑54 (MQ=255)                                                                                                                               tCAAATTAGCCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGAAATAAACCACTTTGCCTGTCATTCCACTACCGGGACtt  >  2:754271/1‑139 (MQ=255)                                                                                                                                        |                                                                                                                                  CCCCTTTATCTTATTTCTGATACTTAGCAGCAAATAAATAACGCGATAAAAAAAGCCAAACGTTTTCGTATTTTACAAACAACCAGAAGCTGGCATCAATTTGTGATCAACCCCACACATTATCCGTCAAATTAGTCTTTTGCAGCCGCGCGGATAATTCTGGCACACTTATTGTTAGTCCCAGGTATAGCTGTGAAAACACCAATCACTTTGGCAAGTCACAGTGAAATAAACCACTTTGCCTGTCATTCCACTACCGGGACTT  >  NZ_CP009273/2999355‑2999619

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑