Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	338,334	T→A	S4T (TCA→ACA)	yahG →	DUF1116 family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	338,334	0	T	A	98.5%	233.0 / ‑4.3	68	S4T (TCA→ACA)	yahG	DUF1116 family protein
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base A (40/27);  total (40/28)
Fisher's exact test for biased strand distribution p-value = 4.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

ATGCCGGAGTGATTCTGGCGAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGTCACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATGTAGAAGTGACTCAACTCGAC  >  NC_000913/338243‑338429                                                                                            |                                                                                                aTGCCGGAGTGATTCTGGCGAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGttt                                                                                         <  2:964344/100‑1 (MQ=255)  tGCCGGAGTGATTCTGGCGAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTa                                                                                        >  2:950525/1‑100 (MQ=255)  tGCCGGAGTGATTCTGGCGAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTa                                                                                        >  2:1234522/1‑100 (MQ=255)  tGCCGGAGTGATTCTGGCGAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTa                                                                                        >  1:479959/1‑100 (MQ=255)   gCCGGAGTGATTCTGGCGAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAg                                                                                       >  2:690623/1‑100 (MQ=255)   gCCGGAGTGATTCTGGCGAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAg                                                                                       <  1:690627/100‑1 (MQ=255)    ccGGAGTGATTCTGGCGAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGc                                                                                      >  2:127041/1‑100 (MQ=255)         gTGATTCTGGCGAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAAGTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAAcc                                                                                 >  2:108148/1‑100 (MQ=255)           gATTCTGGCGAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCAt                                                                               >  1:271909/1‑100 (MQ=255)           gATTCTGGCGAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCAt                                                                               >  2:881046/1‑100 (MQ=255)               cTGGCGAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGaa                                                                           <  1:82886/100‑1 (MQ=255)               cTGGCGAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGaa                                                                           <  2:271906/100‑1 (MQ=255)                    gAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGtta                                                                      <  1:254280/100‑1 (MQ=255)                    gAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGtta                                                                      <  1:515063/100‑1 (MQ=255)                     agcagcagcACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGttat                                                                     >  2:469032/1‑100 (MQ=255)                      gcagcagcaCCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGttatt                                                                    <  2:24510/100‑1 (MQ=255)                      gcagcagcaCCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGttatt                                                                    >  2:808610/1‑100 (MQ=255)                       cagcagcaCCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGttatta                                                                   >  2:12447/1‑100 (MQ=255)                       cagcagcaCCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGttatta                                                                   >  2:247922/1‑100 (MQ=255)                       cagcagcaCCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGttatta                                                                   >  1:533939/1‑100 (MQ=255)                         gcagcaCCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGTCACTGTTTAGCCAACCATTGAACGTTATTAAc                                                                 <  1:116156/100‑1 (MQ=255)                         gcagcaCCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAAc                                                                 <  2:115171/100‑1 (MQ=255)                         gcagcaCCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAAc                                                                 >  1:838086/1‑100 (MQ=255)                         gcagcaCCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAAc                                                                 >  1:447586/1‑100 (MQ=255)                             caCCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCg                                                             <  2:819609/100‑1 (MQ=255)                               ccAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGc                                                           <  2:310901/100‑1 (MQ=255)                                 aaTACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCAt                                                         >  1:13348/1‑100 (MQ=255)                                 aaTACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCAt                                                         >  1:361090/1‑100 (MQ=255)                                  aTACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATc                                                        >  2:167190/1‑100 (MQ=255)                                   tACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCg                                                       >  1:679799/1‑100 (MQ=255)                                     ccGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGcc                                                     >  2:475432/1‑100 (MQ=255)                                        gATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATg                                                  <  2:753893/100‑1 (MQ=255)                                             cTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAg                                             >  1:670086/1‑100 (MQ=255)                                              tGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGc                                            <  1:402366/100‑1 (MQ=255)                                              tGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGc                                            <  1:1186404/100‑1 (MQ=255)                                                gcgcGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGa                                          <  1:1118891/100‑1 (MQ=255)                                                      gAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCt                                    >  2:1028280/1‑100 (MQ=255)                                                       aaTTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTg                                   <  1:469036/100‑1 (MQ=255)                                                         tttATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGaa                                 >  1:746745/1‑100 (MQ=255)                                                             tCTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAag                             >  2:819963/1‑100 (MQ=255)                                                             ncTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAag                             >  2:179215/2‑100 (MQ=255)                                                              cTGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAagc                            <  1:31750/100‑1 (MQ=255)                                                               tGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAagca                           >  2:864598/1‑100 (MQ=255)                                                               tGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAagca                           >  1:818883/1‑100 (MQ=255)                                                               tGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAagca                           <  2:225525/100‑1 (MQ=255)                                                               tGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAagca                           >  1:1086837/1‑100 (MQ=255)                                                               tGCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAagca                           <  1:1135514/100‑1 (MQ=255)                                                                gCAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAagcag                          <  2:819974/100‑1 (MQ=255)                                                                 cAAAGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAagcagc                         >  2:655142/1‑100 (MQ=255)                                                                   aaGGGGAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCAt                       >  2:72455/1‑100 (MQ=255)                                                                     ggggAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATg                      >  2:645408/1‑99 (MQ=255)                                                                     ggggAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATGt                     >  1:50434/1‑100 (MQ=255)                                                                      gggAGGAAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATGTa                    <  2:721167/100‑1 (MQ=255)                                                                        gaggaAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATGTAGa                  >  2:152352/1‑100 (MQ=255)                                                                         aggaAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATGTAGaa                 >  1:980641/1‑100 (MQ=255)                                                                          ggaAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATGTAGAAg                <  2:1183317/100‑1 (MQ=255)                                                                          ggaAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATGTAGAAg                >  1:381096/1‑100 (MQ=255)                                                                          ggaAGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATGTAGAAg                >  2:343423/1‑100 (MQ=255)                                                                           gaAGCCTGATGAGCCAGACAATGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAACAGCAGCATGTAGAAGt               >  2:797798/1‑100 (MQ=255)                                                                             aGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATGTAGAAGTGa             <  1:645412/100‑1 (MQ=255)                                                                             aGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATGTAGAAGTGa             >  1:816503/1‑100 (MQ=255)                                                                             aGCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATGTAGAAGTGa             >  1:898845/1‑100 (MQ=255)                                                                              gCCTGATGAGCCAGACACTGTTTAGCCAACCATTGAACTTTATTAACGTCGGCATCGCCATGTTTAACGAAAAAATAAAAAAGCAGCATGTAGAAGTg              <  2:1086827/98‑1 (MQ=255)                                                                               ccTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATGTAGAAGTGACt           <  2:1077686/100‑1 (MQ=255)                                                                                cTGATGAGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATGTAGAAGTGACTc          <  1:475436/100‑1 (MQ=255)                                                                                      aGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAGAAAGCAGCATGTAGAAGTGACTCAACTCg    >  2:432408/1‑100 (MQ=255)                                                                                      aGCCAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATGTAGAAGTGACTCAACTCg    <  1:179217/100‑1 (MQ=255)                                                                                        ccAGACACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGTAAAAGCAGCATGTAGAAGTGACTCAACTCGAc  <  1:1234533/100‑1 (MQ=255)                                                                                            |                                                                                                ATGCCGGAGTGATTCTGGCGAGCAGCAGCACCAATACCGGATTGCTGGCGCGTGAATTTATCTGCAAAGGGGAGGAAGCCTGATGAGCCAGTCACTGTTTAGCCAACCATTGAACGTTATTAACGTCGGCATCGCCATGTTTAGCGATGACCTGAAAAAGCAGCATGTAGAAGTGACTCAACTCGAC  >  NC_000913/338243‑338429

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑