Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,606,417	A→T	9.1%	intergenic (‑16/+252)	leuQ ← / ← rsmC	tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase, SAM‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,606,417	0	A	T	9.1%	220.6 / 10.3	66	intergenic (‑16/+252)	leuQ/rsmC	tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase, SAM‑dependent
Reads supporting (aligned to +/- strand):  ref base A (30/30);  new base T (3/3);  total (33/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01

AATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGCTGGAAAAATGTCCATCAGGAAACTAG  >  NC_000913/4606270‑4606525                                                                                                                                                    |                                                                                                             aaTTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTa                                                                                                              <  2:816271/148‑1 (MQ=255)      cGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAg                                                                                                         >  1:662784/1‑148 (MQ=255)                                                   cGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGt                                                            <  2:662784/148‑1 (MQ=255)                                                      ggggggggACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTTTTAAGAATTg                                                                                                    >  4:334819/1‑105 (MQ=255)                                                      ggggggggACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTTTTAAGAATTg                                                                                                    <  3:334819/105‑1 (MQ=255)                                                              aCTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAAt                                                 >  2:118686/1‑148 (MQ=255)                                                               cTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCtttt                                                               >  3:1022631/1‑133 (MQ=255)                                                               cTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCtttt                                                               <  4:1022631/133‑1 (MQ=255)                                                                 tGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTAcc                                                                                               >  3:1083296/1‑99 (MQ=255)                                                                 tGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTAcc                                                                                               <  4:1083296/99‑1 (MQ=255)                                                                   aaCCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCtttt                                                               >  4:470098/1‑129 (MQ=255)                                                                   aaCCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCtttt                                                               <  3:470098/129‑1 (MQ=255)                                                                       cccACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGaa                                                                                                       >  4:1115027/1‑85 (MQ=255)                                                                       cccACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGaa                                                                                                       <  3:1115027/85‑1 (MQ=255)                                                                                 tAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGgcg                                                                                      <  2:548043/92‑1 (MQ=255)                                                                                 tAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGgcg                                                                                      >  1:548043/1‑92 (MQ=255)                                                                                 tAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCa                                                          >  2:131206/1‑120 (MQ=255)                                                                                 tAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCa                                                          <  1:131206/120‑1 (MQ=255)                                                                                   aGGACCCTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGgtg                                   <  4:1035499/141‑1 (MQ=255)                                                                                   aGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGgtg                                   >  3:1035499/1‑141 (MQ=255)                                                                                       cacTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGt                                                                             <  2:459758/95‑1 (MQ=255)                                                                                       cacTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGt                                                                             >  1:459758/1‑95 (MQ=255)                                                                                         cTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTaaaa                                                                                                           >  2:515010/1‑63 (MQ=255)                                                                                         cTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTaaaa                                                                                                           <  1:515010/63‑1 (MQ=255)                                                                                         cTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGt                                                     >  2:444547/1‑117 (MQ=255)                                                                                         cTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGt                                                     <  1:444547/117‑1 (MQ=255)                                                                                           aaCACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACaga                                       <  3:179074/129‑1 (MQ=255)                                                                                           aaCACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACaga                                       >  4:179074/1‑129 (MQ=255)                                                                                           aaCACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGCTGGaaaaa                    <  1:118686/148‑1 (MQ=255)                                                                                                 tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCtt                                                                 >  2:647274/1‑97 (MQ=255)                                                                                                 tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCtt                                                                 <  1:647274/97‑1 (MQ=255)                                                                                                 tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAACTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGgtg                                   >  3:860912/1‑127 (MQ=255)                                                                                                 tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAACTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGgtg                                   <  4:860912/127‑1 (MQ=255)                                                                                                  gAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTa                                                   >  3:210345/1‑110 (MQ=255)                                                                                                  gAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTa                                                   <  4:210345/110‑1 (MQ=255)                                                                                                                  ccAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGtttt                                                                       <  3:1038834/74‑1 (MQ=255)                                                                                                                  ccAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGtttt                                                                       >  4:1038834/1‑74 (MQ=255)                                                                                                                  ccAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACaga                                       <  4:760022/106‑1 (MQ=255)                                                                                                                  ccAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACaga                                       >  3:760022/1‑106 (MQ=255)                                                                                                                  ccAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGCt                           >  4:55637/1‑118 (MQ=255)                                                                                                                  ccAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGCt                           <  3:55637/118‑1 (MQ=255)                                                                                                                   cAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCt                                                                                >  4:763293/1‑64 (MQ=255)                                                                                                                   cAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCt                                                                                <  3:763293/64‑1 (MQ=255)                                                                                                                   cAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCg                                                             >  4:795860/1‑83 (MQ=255)                                                                                                                   cAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCg                                                             <  3:795860/83‑1 (MQ=255)                                                                                                                   cAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCa                                                          <  2:900045/86‑1 (MQ=255)                                                                                                                   cAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCa                                                          >  1:900045/1‑86 (MQ=255)                                                                                                                   cAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGCTGGAAAAATGTCCATCAGGAAACTAg  <  4:380958/142‑1 (MQ=255)                                                                                                                   cAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGCTGGAAAAATGTCCATCAGGAAACTAg  >  3:380958/1‑142 (MQ=255)                                                                                                                    aaTTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGt                                                                             >  4:1112382/1‑66 (MQ=255)                                                                                                                    aaTTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGt                                                                             <  3:1112382/66‑1 (MQ=255)                                                                                                                      ttCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACag                                        >  3:604203/1‑101 (MQ=255)                                                                                                                      ttCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACag                                        <  4:604203/101‑1 (MQ=255)                                                                                                                           ccACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGgt                                    <  3:942600/100‑1 (MQ=255)                                                                                                                           ccACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGgt                                    <  3:766954/100‑1 (MQ=255)                                                                                                                           ccACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGgt                                    >  4:942600/1‑100 (MQ=255)                                                                                                                           ccACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGgt                                    >  4:766954/1‑100 (MQ=255)                                                                                                                            cACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGCTGGAAAAATGTCCATc            >  1:593328/1‑123 (MQ=255)                                                                                                                            cACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGCTGGAAAAATGTCCATc            <  2:593328/123‑1 (MQ=255)                                                                                                                                ttCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGCTGGAAAAAt                   <  4:985112/112‑1 (MQ=255)                                                                                                                                ttCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGCTGGAAAAAt                   >  3:985112/1‑112 (MQ=255)                                                                                                                                         cATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGCTGGAAAAATGTCCa              >  1:406956/1‑108 (MQ=255)                                                                                                                                         cATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGCTGGAAAAATGTCCa              <  2:406956/108‑1 (MQ=255)                                                                                                                                           gcAATTCTTTTTAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGc                            <  2:605028/91‑1 (MQ=255)                                                                                                                                           gcAATTCTTTTTAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGc                            >  3:1139753/2‑92 (MQ=255)                                                                                                                                           gcAATTCTTTTTAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGc                            <  4:1139753/91‑1 (MQ=255)                                                                                                                                           gcAATTCTTTTTAAGAATTGCTACCACGGAGGCGCATTCTAGTGGGTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGc                            >  1:605028/2‑92 (MQ=255)                                                                                                                                            cAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGCTGGAAAAATGTCCATCAGGAAACTAg  >  1:1096961/1‑117 (MQ=255)                                                                                                                                            cAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGCTGGAAAAATGTCCATCAGGAAACTAg  <  2:1096961/117‑1 (MQ=255)                                                                                                                                                    |                                                                                                             AATTCCGCCACCTTCGCCCAGTGCGAGCAATATCAACGTGGTTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCATACCATCAATTCTTAAAAAGAATTGCTACCACGGAGGCGCATTCTAGTGGTTTTCAGCTTTTCGTCAATAGTTAATTATCGACAGAGGTGTAATTGCTGGAAAAATGTCCATCAGGAAACTAG  >  NC_000913/4606270‑4606525

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑