Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,317,027	C→T	*950* (TAG→TAA)	rcsC ←	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,317,027	0	C	T	98.2%	168.8 / NA	54	*950* (TAG→TAA)	rcsC	hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (25/28);  total (26/28)
Fisher's exact test for biased strand distribution p-value = 4.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGGCCTACGATTCCCATTATTTCAACAAATTACATTAAAGTAGGCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCCTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTCGACAGGCAGCTGTCCATACCGGACTCCAGACACCGCTGCTTCTCTTCAGCCAACGCA  >  NC_000913/2316908‑2317162                                                                                                                        |                                                                                                                                        ccGGCCTACGATTCCCATTATTTCAACAAATTACATTAAAGTAGGCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGTACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTcc                                                                                                                      >  1:173964/1‑139 (MQ=255)        aCGATTCCCATTATTTCAACAAATTACATTAAAGTAGGCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCct                                                                                                               <  1:669015/139‑1 (MQ=255)           aTTCCCATTATTTCAACAAATTACATTAAAGTAGGCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCtctc                                                                                                            <  2:91266/139‑1 (MQ=255)             tCCCATTATTTCAACAAATTACATTAAAGTAGGCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCgg                                                                                                          <  1:1348771/139‑1 (MQ=255)               ccATTATTTCAACAAATTACATTAAAGTAGGCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCcgcg                                                                                                                            <  1:268802/119‑1 (MQ=255)               ccATTATTTCAACAAATTACATTAAAGTAGGCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCcgcg                                                                                                                            >  2:268802/1‑119 (MQ=255)                       tCAACAAATTACATTAAAGTAGGCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGaa                                                                                                                                   <  2:328278/104‑1 (MQ=255)                       tCAACAAATTACATTAAAGTAGGCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGaa                                                                                                                                   >  1:328278/1‑104 (MQ=255)                         aacaaATTACATTAAAGTAGGCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCa                                                                                              >  1:254464/1‑139 (MQ=255)                          acaaATTACATTAAAGTAGGCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAg                                                                                             >  1:1176679/1‑139 (MQ=255)                                       aaGTAGGCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGtt                                                                                     >  1:1266404/1‑134 (MQ=255)                                       aaGTAGGCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGtt                                                                                     <  2:1266404/134‑1 (MQ=255)                                            ggCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGt                                                                                          >  1:529581/1‑124 (MQ=255)                                            ggCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGt                                                                                          <  2:529581/124‑1 (MQ=255)                                            ggCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATc                                                                           >  1:502616/1‑139 (MQ=255)                                             gCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATcc                                                                          >  2:688240/1‑139 (MQ=255)                                             gCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACAAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTc                                                                                         <  2:951651/124‑1 (MQ=255)                                             gCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACAAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTc                                                                                         >  1:951651/1‑124 (MQ=255)                                                 gATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCg                                                                      >  2:1081866/1‑139 (MQ=255)                                                  aTAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGAc                                                                                                                  <  1:481343/94‑1 (MQ=255)                                                  aTAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGAc                                                                                                                  >  2:481343/1‑94 (MQ=255)                                                       aCGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCg                                                                >  1:433872/1‑139 (MQ=255)                                                        agcgTCAGGGTCGCATCTGGCATTTGCACTGAATGCCGGATGTGGCGTAAACGCCTTATCTGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCgg                                                               <  2:874982/138‑1 (MQ=255)                                                            tCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTg                                                                                                                    <  1:1039930/82‑1 (MQ=255)                                                            tCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTg                                                                                                                    >  2:1039930/1‑82 (MQ=255)                                                            tCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTAt                                                                                 >  2:30365/1‑117 (MQ=255)                                                            tCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTAt                                                                                 <  1:30365/117‑1 (MQ=255)                                                            tCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTc                                                           >  1:701449/1‑139 (MQ=255)                                                                tgTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTCGACa                                                       <  1:1081866/138‑1 (MQ=255)                                                                 gTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCg                                                                                           >  1:405849/1‑102 (MQ=255)                                                                 gTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCg                                                                                           <  2:405849/102‑1 (MQ=255)                                                                     cATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTCGACAGGCAg                                                  <  2:254464/139‑1 (MQ=255)                                                                     cATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTCGACAGGCAg                                                  <  2:1176679/139‑1 (MQ=255)                                                                     cATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTCGACAGGCAg                                                  <  2:502616/139‑1 (MQ=255)                                                                     cATCTGGAATTTGCACTGAATGCCCGATGTGGCGTAAACGCCTTATCCGTCCTACGAATCCCGCGATTTCCTGACCATCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCAGCTTCGACAGGcct                                                  >  1:874982/1‑137 (MQ=38)                                                                         tGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTCGACAGGCAGCTGt                                              <  2:127931/139‑1 (MQ=255)                                                                          ggCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCct                                                                                                               <  2:1311505/73‑1 (MQ=255)                                                                          ggCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCct                                                                                                               >  1:1311505/1‑73 (MQ=255)                                                                              tttGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTCGACAGGCAGCTGTCCATa                                         <  2:1006357/139‑1 (MQ=255)                                                                                tGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTCGACAGGCAGCTGTCCATAcc                                       <  2:1185568/139‑1 (MQ=255)                                                                                  cACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTCGACAGGCAg                                                  >  2:177149/1‑126 (MQ=255)                                                                                  cACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTCGACAGGCAg                                                  <  1:177149/126‑1 (MQ=255)                                                                                     tGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTCGACAGGCAGCTGTCCATACCGGACt                                  >  1:651111/1‑139 (MQ=255)                                                                                         tGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCtctc                                                                                                            <  2:38918/61‑1 (MQ=255)                                                                                         tGCCGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCtctc                                                                                                            >  1:38918/1‑61 (MQ=255)                                                                                            cGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTCGACAGGCAGCTGTCCATACCGGACTCCAGaca                           >  1:85184/1‑139 (MQ=255)                                                                                            cGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCCCTCGGCATATAACGTCAGCGTCTGTTTTAt                                                                                 >  2:930003/1‑85 (MQ=38)                                                                                            cGGATGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCCCTCGGCATATAACGTCAGCGTCTGTTTTAt                                                                                 <  1:930003/85‑1 (MQ=38)                                                                                                tGCGGCGTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTCGACAGGCAGCTGTCCATACCGGACTCCAGACACCgc                       <  2:433872/139‑1 (MQ=255)                                                                                                    gcgTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCt                                                                                                                     <  2:1010979/41‑1 (MQ=255)                                                                                                    gcgTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCt                                                                                                                     >  1:1010979/1‑41 (MQ=255)                                                                                                    gcgTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTa                                                                   >  2:1373370/1‑91 (MQ=255)                                                                                                    gcgTAAACGCCTTATCCGTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTa                                                                   <  1:1373370/91‑1 (MQ=255)                                                                                                                     gTCTTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTCGACAGGCAGCTGTCCATACCGGACTCCAGACACCGCTGCTTCTCTTCAGCCAACGCa  <  1:688240/139‑1 (MQ=255)                                                                                                                        |                                                                                                                                        CCGGCCTACGATTCCCATTATTTCAACAAATTACATTAAAGTAGGCCAGATAAGACGCGTCAGCGTCGCATCTGGCATTTGCACTGAATGCCGGATGCGGCGTAAACGCCTTATCCGTCCTACGAATCCCGCGATTTCCTGACCCTCTCGGCATATAACGTCAGCGTCTGTTTTATCACATCCAGCGTTACCGGCTTCGACAGGCAGCTGTCCATACCGGACTCCAGACACCGCTGCTTCTCTTCAGCCAACGCA  >  NC_000913/2316908‑2317162

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑