Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,406,853	C→A	11.3%	A315S (GCC→TCC)	dgcM ←	diguanylate cyclase DgcM

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,406,853	0	C	A	11.3%	80.4 / 2.2	40	A315S (GCC→TCC)	dgcM	diguanylate cyclase DgcM
Reads supporting (aligned to +/- strand):  ref base C (22/13);  new base A (3/2);  total (25/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.38e-01

CTTTTGCCACGCTTACGCGGATAGTTTCAGCCAGCGAAAGCGCGGTATCCAGTGGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATCGTTAATGTGTTTAAAACGATCGGTGTCGATGAGCAACAAGCTGTAATCCTGAGCGATGGCGAGATGCTGCATTTGGCCTGGTTCCGTAAT  >  NC_000913/1406712‑1406988                                                                                                                                              |                                                                                                                                        cgtttGCCACGCTTACGCGGATAGTTTCAGCCAGCGAAAGCGCGGTATCCAGTGGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAAGCGCCGTTGCGAGCGCAACTTTCGAGGGTGCGGGCg                                                                                                                                        <  1:452877/141‑1 (MQ=255)     tGCCACGCTTACGCGGATAGTTTCAGCCAGCGAAAGCGCGGTATCCAGTAGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACAAACAAGTCCAGTCGGTCTCAACTTTCGAGGGTGCGGGCGAggg                                                                                                                                    <  2:630736/143‑1 (MQ=255)         ccgctgccgcgGATAGTCTGGTCCCTCGAAAGCGCGGTATCCGCTCCGGTTCTTGGTAGCAATAAGACAATCGCTTCGCCTCTTCACGGAAACACCAAATCGCCTTTGCGACCGCAACTTTCGAGGGTGCGGGCGAGGGCGCa                                                                                                                                <  2:250564/136‑1 (MQ=255)         aCGCTTACGCGGTTAGTTTGAGCCATCGAAAGCGCGTTATCCAGTGGGGTTCTTGGTAGCAATAAGACATACTCTTCGCCTCCCCGACGAAACACCAAATCGCCGTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCa                                                                                                                                <  2:258341/143‑1 (MQ=255)              tACGCGGATAGTTTCAGCCAGCGAAAGCGCGGTATCCAGTGGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAaca                                                                                                                           <  1:318793/143‑1 (MQ=255)               aCGCGGATAGTTTCAGCCAGCGAAAGCGCGGTATCCAGTGGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAacac                                                                                                                          >  1:668353/1‑143 (MQ=255)               aCGCGGATAGTTTCAGCCAGCGAAAGCGCGGTATCCAGTGGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACAAGATCGCCTATGCGAGCGCAACATTCGAGGGTGAGGGCGAGGGAGAATAacac                                                                                                                          >  2:426116/1‑143 (MQ=255)                   ggATAGTTTCAGCCAGCGAAAGCGCGGTATCCAGTGGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGCAACACCACATCGCCTTTGCGAGCGCAACTTTCGCGGGTGCGAGCGAGAGCGCATAacacataa                                                                                                                      >  1:522738/1‑139 (MQ=255)                   ggATAGTTTCAGCCAGCGAAAGCGCAGTATCCAGTGGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTCCGAGCGCAACTTGCGAGGGTCCGGCCGAGGCCTCAACACACCtca                                                                                                                      >  2:564203/1‑143 (MQ=255)                         tttCAGCCAGCGAAAGCGCGGTATCCAGTGGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCt                                                                                                                <  2:591030/143‑1 (MQ=255)                           tCAGCCAGCGAAAGCGCGGTATCCAGTGGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCACCGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCGTAAAACCTCATCACCttt                                                                                                              >  1:99591/1‑143 (MQ=255)                                   cGAAAGCGCGGTATCCAGTGGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGGAACTTTCGAGGGTGCGGGCGAGGGCGCATAACAACCCATCACATTTAGAGTGcc                                                                                                      >  2:728574/1‑143 (MQ=255)                                      aaGCGCGGTATCCAGTGGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAATGGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGAGAGGGCGCATAACACCTCATCCCCTTGGGAATGCCCAt                                                                                                   >  2:493508/1‑143 (MQ=255)                                      aaGCGCGGTATCCAGTGGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGAGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCAt                                                                                                   >  2:107273/1‑143 (MQ=255)                                           cgGTATCCAGTGGGATTCTTAGTAGCAATAAGAAAAACTCTTCGCCGCCCCAACGAGACACCAAATCGACATTGCGAGCACAACATTCGAAGGAGAGGGCACGGGCGCATAACACCTCATCACCTCTAGAATGCCCATAaaga                                                                                              >  2:768836/1‑143 (MQ=255)                                            ggTATCCAGTGGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTCGAATGCCCATATAGAt                                                                                             >  1:369817/1‑143 (MQ=255)                                             gTATCCGGTGGGGTTCTTGGTAGCAATAAGACAAGCTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATc                                                                                            <  2:143395/143‑1 (MQ=255)                                                     tGGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGGGGGCGCGTAACACCTCATCACCTTTCGAATGCCCATAGATGTCGTCACtgt                                                                                    >  1:198489/1‑143 (MQ=255)                                                      ggggTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATCGTTAAtgtg                                                                                   <  2:62996/143‑1 (MQ=255)                                                      ggcgTTATTGGTAGCAATAAGACAAACGCTTCGCCTCCCCAACGACACACCAAATCGCCTTTGCGAGCGCACCTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCTTCACCTTTAGAATGCCCATAGAGATCGTTAAtgtg                                                                                   <  2:165085/140‑1 (MQ=255)                                                          ttCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATCACACCTCATCACCTTTCGAATGCCCATAGAGAGCGTTTGTGTGCTTa                                                                               >  1:295310/1‑143 (MQ=255)                                                          ttCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGCGCTCGTTAATGTGTTTa                                                                               >  2:744259/1‑143 (MQ=255)                                                            cTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGACGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATCGCTAATGTGTATaaa                                                                             >  2:334853/1‑143 (MQ=255)                                                             ttGGTAGCAATAAGACAACCTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGTGCGATGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATCGTTAATGTGTTTaaaa                                                                            <  1:281601/143‑1 (MQ=255)                                                                  aGCAAGAAGACAAGCTCTTCGCCTCCCCAACGAGACGCCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATCGTTAATGTGTTTAAAACGATc                                                                       <  2:522334/143‑1 (MQ=255)                                                                           aCAAACTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAAATTTCGAGGGTGCGGGCGCGGGCACATAACACCTCATCACCTTTAGAATGCCCGTAGGACTCGTTAAGGTGTTTAAAACGATCCgtcgcgca                                                              >  1:85419/1‑137 (MQ=255)                                                                                  ctTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACGTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATCGTTAATGTGTTTAAAACGATCGGACGCGATGAAcaaa                                                       >  2:206159/1‑142 (MQ=255)                                                                                   ttCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGCTCGTTAATGTGTTTAAAACGATCGGTGACGAAGAGcaaca                                                      >  1:85167/1‑143 (MQ=255)                                                                                           cccAACGAAACACCAAATCACCTTTGCAAGCTAAATTTTCGAGGGTGCGGGAGGTGATGGCAATTACATAAGAGCCGTTGGAAGGTCCATAGAGGTCGTTAAGGTGTTTGATACGATCGGTGTTAGTCAGCGACAAGGTGTaa                                              >  2:159637/1‑143 (MQ=255)                                                                                              aaCGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATCGTTAATGTGTTTAAAACGATCGGTGTCGATGAGCAACAAGCTGTAATcc                                           >  2:721921/1‑143 (MQ=255)                                                                                                 cacgttccAAATCGCCTGTGCTACCCCAACTTTCGATGGTCCGGGCGAGGGCTCATACCACCTCATCACCTATATAATGCCCATAGATATCGTTAATGTGTTTAATACGATCGGTGTCGATGAGCAACAAGCTGTAATCCCGa                                        <  2:397018/137‑1 (MQ=255)                                                                                                           aTCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCGCCTTTAGGATGCCCATAGAGAGCGTTACTGTGTTTAAAACGATCGGTGTCGATGAGCAACAAGCTGTAATCCCTAGCGATggaca                              >  1:438120/1‑140 (MQ=255)                                                                                                                cTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATCGTTAATGTGTTTAAAACGATCGGTGTCGATGCGCAACCAGCTGTCATCCTGTGCGATGGCGAGAtgc                         >  1:40394/1‑143 (MQ=255)                                                                                                                 tttGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATCGTTAATGTGTTTAAAACGATCGGTGTCGATGAGCATCTAGCTGTGATTCTGAGCGATGGCTAGAtgct                        >  1:215/1‑143 (MQ=255)                                                                                                                       aGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATCGTTAATGTGTTTAAAACGATCGGTGTCGATGAGCAACAAGCTGTAATCCTGAGCGATGGCGAGATGCTGCAttt                  >  2:180435/1‑143 (MQ=255)                                                                                                                         cgcAACTTTCGAGGGTGCGGGAGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATCGTTAATGTGTTTAAAACGATCGGTGTCGATGAGCAACAAGCTGTAATCCTGAGCGATGGCGAGATGCTGCATTTgg                <  1:107273/143‑1 (MQ=255)                                                                                                                         cgcAACTTGCGAGGGTGCGGGAGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATCGTTAATGTGTTTAAAACGATCGGTGTCGATGAGCAACAAGCTGTAATCCTGAGCGATGGCGAGATGCTGCATTTgg                <  1:493508/143‑1 (MQ=255)                                                                                                                            aaCTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATCGTTAATGTGTTTAAAACGATCGGTGTCGATGAGCAACAAGCTGTAATCCTGAGCGATGGCGAGATGCTGCATTTGGCCt             >  2:350875/1‑143 (MQ=255)                                                                                                                               tttCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATCGTTAATGTGTTTAAAACGATCGGTGTCGATGAGCAACAAGCTGTAATCCTGAGCGATGGCGAGATGCTGCATTTGGCCTGGt          >  1:115009/1‑143 (MQ=255)                                                                                                                                  cGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTAGTATGCCCATATAGATCGTTAATGTGTTTAAAACGATCGGTGTCGATGAGCAACAAGCTGTAATCCTGAGCGATGGCGAGATGCTGCATTTGGCCTGGTTcc       <  1:521205/143‑1 (MQ=255)                                                                                                                                       gtgcgtgcGAGGGCGCATAACACCTCATCACCTTTAGAATGCTCATAGAGATCGTTAATGTGTTTAAAACGATCGGTGTCGATGAGCAACAAGCTGTAATCCTGAGCGATGGCGAGATGCTGCATTTGGCCTGGTTCCGTAAt  <  2:693495/143‑1 (MQ=255)                                                                                                                                       gtgcgtgcGAGGGCGCATAACACCGCATCACCTGTAGGATGCCCATAGAGATCGTTAATGTGTTTAGAACGATCGGTGTCGATGAGCAACAAGCTGTAATCCTGAGCGATGGCGAGATGCTGCATTTGGCCTGGTTCCGTAAt  <  2:547697/143‑1 (MQ=255)                                                                                                                                              |                                                                                                                                        CTTTTGCCACGCTTACGCGGATAGTTTCAGCCAGCGAAAGCGCGGTATCCAGTGGGGTTCTTGGTAGCAATAAGACAAACTCTTCGCCTCCCCAACGAAACACCAAATCGCCTTTGCGAGCGCAACTTTCGAGGGTGCGGGCGAGGGCGCATAACACCTCATCACCTTTAGAATGCCCATAGAGATCGTTAATGTGTTTAAAACGATCGGTGTCGATGAGCAACAAGCTGTAATCCTGAGCGATGGCGAGATGCTGCATTTGGCCTGGTTCCGTAAT  >  NC_000913/1406712‑1406988

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑