Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	BX571857	423,924	G→A	10.3%	intergenic (‑183/‑171)	SAS0378 ← / → SAS0379	hypothetical protein/conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	BX571857	423,924	0	G	A	10.3%	302.8 / 26.6	87	intergenic (‑183/‑171)	SAS0378/SAS0379	hypothetical protein/conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (54/24);  new base A (7/2);  total (61/26)
Fisher's exact test for biased strand distribution p-value = 7.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.78e-01

GTTTAAAAGCATTATGCAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAACACAATTGGGTTGGTAGTCCC  >  BX571857/423832‑424017                                                                                             |                                                                                              gTTTAAAAGCATTATGCAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTATAAt                                                                                           >  1:1534576/1‑97 (MQ=255)  tttAAAAGCATTATGCAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAAtg                                                                                          <  1:201867/97‑1 (MQ=255)   ttAAAAGCATTATGCAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAAtgt                                                                                         >  1:332526/1‑97 (MQ=255)    tAAAAGCATTATGCAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTTTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAAtgtg                                                                                        <  1:502462/97‑1 (MQ=255)    tAAAAGCATTATGCAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAAtgtg                                                                                        >  1:1215274/1‑97 (MQ=255)     aaaaGCATTATGCAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGa                                                                                       >  2:1201769/1‑97 (MQ=255)      aaaGCATTATGCAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGaa                                                                                      >  1:707957/1‑97 (MQ=255)      aaaGCATTATGCAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTATAATGTGaa                                                                                      <  2:735048/97‑1 (MQ=255)            ttATGCAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTa                                                                                >  2:679360/1‑97 (MQ=255)              aTGCAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTTAATTTTTaaa                                                                              >  2:690958/1‑97 (MQ=255)              aTGCAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTaaa                                                                              >  2:622602/1‑97 (MQ=255)              aTGCAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTaaa                                                                              >  2:623067/1‑97 (MQ=255)                gCAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAAt                                                                            <  1:20875/97‑1 (MQ=255)                 cAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAAtt                                                                           >  1:441698/1‑97 (MQ=255)                   ttGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAAGATTTTATTAGCGTCATTTACATCTACCTTCTGTAATGTGAATTCTTAAGATTAc                                                                         <  2:1134068/96‑1 (MQ=255)                   aTGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTAc                                                                         >  1:1377213/1‑97 (MQ=255)                   aTGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTATAATGTGAATTTTTAAAATTAc                                                                         >  1:683540/1‑97 (MQ=255)                    tGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACa                                                                        >  1:257729/1‑97 (MQ=255)                     gCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAg                                                                       >  1:1091876/1‑97 (MQ=255)                     gCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAg                                                                       >  2:378400/1‑97 (MQ=255)                     gCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAg                                                                       >  2:89523/1‑97 (MQ=255)                     gCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAg                                                                       >  2:90394/1‑97 (MQ=255)                      ccAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAga                                                                      >  2:1292714/1‑96 (MQ=255)                      ccAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGt                                                                      >  2:1093073/1‑97 (MQ=255)                      ccAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGt                                                                      <  1:899751/97‑1 (MQ=255)                       cAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGtt                                                                     <  2:202206/97‑1 (MQ=255)                        aaTCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGttt                                                                    >  2:1518741/1‑97 (MQ=255)                        aaTCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGttt                                                                    >  2:615904/1‑97 (MQ=255)                         aTCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTa                                                                   <  1:1222391/97‑1 (MQ=255)                         aTCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTa                                                                   <  2:44681/97‑1 (MQ=255)                           cAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACa                                                                 >  1:390698/1‑97 (MQ=255)                           cAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACa                                                                 >  1:1126204/1‑97 (MQ=255)                                cTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTATAATGTGAATTTTTAAAATTACAGTTTACATGTaa                                                            >  1:1406032/1‑97 (MQ=255)                                 tAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAAc                                                           <  1:1214285/97‑1 (MQ=255)                                 tAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTATAATGTGAATTTTTAAAATTACAGTTTACATGTAAc                                                           >  1:143153/1‑97 (MQ=255)                                  aaTGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACg                                                          >  1:1356473/1‑97 (MQ=255)                                  aaTGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACg                                                          >  2:164632/1‑97 (MQ=255)                                  aaTGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACg                                                          <  1:585590/97‑1 (MQ=255)                                   aTGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGt                                                         >  1:1451665/1‑97 (MQ=255)                                   aTGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGt                                                         >  2:1039673/1‑97 (MQ=255)                                      gggTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTtgt                                                      <  1:1560700/97‑1 (MQ=255)                                      gggTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTtgt                                                      >  2:1054878/1‑97 (MQ=255)                                       ggTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTtgtg                                                     >  2:1153625/1‑97 (MQ=255)                                        gtgtAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGc                                                    <  1:1254283/97‑1 (MQ=255)                                         tgtAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCa                                                   <  1:465459/97‑1 (MQ=255)                                           tAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAat                                                 <  2:1311877/97‑1 (MQ=255)                                           tAAGTATTTCCCGGTTAATATTTTCTTAGCGTTATTTACATATACCTTCTGTCCTGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAat                                                 >  2:146020/1‑97 (MQ=255)                                            aaGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAata                                                <  2:463146/97‑1 (MQ=255)                                             aGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAatat                                               >  2:29638/1‑97 (MQ=255)                                             aGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAatat                                               >  2:794319/1‑97 (MQ=255)                                               tATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAatatat                                             >  2:358199/1‑97 (MQ=255)                                                aTTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTATAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATAtt                                            >  2:301402/1‑97 (MQ=255)                                                  ttCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCACTATATTCt                                          >  1:1488458/1‑97 (MQ=255)                                                  ttCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCt                                          <  2:301541/97‑1 (MQ=255)                                                   tCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTg                                         >  1:335928/1‑97 (MQ=255)                                                    cccTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGt                                        >  1:544863/1‑97 (MQ=255)                                                       tGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGtata                                     >  1:1444156/1‑97 (MQ=255)                                                           aaTATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGCATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGtatatata                                 >  2:1086555/1‑95 (MQ=255)                                                            atatTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGaa                                <  1:1452818/97‑1 (MQ=255)                                                              atTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAgt                              >  2:64238/1‑97 (MQ=255)                                                                tttATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAgtgt                            >  2:1087934/1‑97 (MQ=255)                                                                 ttattaGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTa                           >  1:14161/1‑97 (MQ=255)                                                                 ttattaGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTa                           >  2:314349/1‑97 (MQ=255)                                                                 ttattaGCGTTATTTACATATACCTTCTATAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTa                           >  1:836442/1‑97 (MQ=255)                                                                  tattaGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTaa                          <  1:991890/97‑1 (MQ=255)                                                                    ttaGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTaaaa                        >  1:57202/1‑97 (MQ=255)                                                                      aGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAac                      >  1:647870/1‑97 (MQ=255)                                                                      aGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAac                      >  1:1569178/1‑97 (MQ=255)                                                                      aGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAac                      >  1:227396/1‑97 (MQ=255)                                                                      aGCGTTATTTACATATACCTTCTATAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAac                      >  1:287557/1‑97 (MQ=255)                                                                        cGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAacac                    <  1:357181/97‑1 (MQ=255)                                                                         gTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAAcaca                   >  2:923328/1‑97 (MQ=255)                                                                         gTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAAcaca                   <  2:472429/97‑1 (MQ=255)                                                                         gTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAAcaca                   >  1:1147599/1‑97 (MQ=255)                                                                          ttATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAACACaa                  <  2:247317/97‑1 (MQ=255)                                                                          ttATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAACACaa                  >  2:904099/1‑97 (MQ=255)                                                                            aTTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAACACAAtt                >  2:1188469/1‑97 (MQ=255)                                                                             tttACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAACACAATTg               <  1:1249357/97‑1 (MQ=255)                                                                              ttACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAACACAATTgg              >  1:277533/1‑97 (MQ=255)                                                                               tACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAACACAATTggg             >  2:58386/1‑97 (MQ=255)                                                                               tACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAACACAATTggg             >  1:1011769/1‑97 (MQ=255)                                                                                      aCCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAACACAATTGGGTTGGTAg      <  1:152198/97‑1 (MQ=255)                                                                                      aCCTTCTATAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAACACAATTGGGTTGGTAg      <  2:223187/97‑1 (MQ=255)                                                                                       ccTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAACACAATTGGGTTGGTAGt     <  1:776075/97‑1 (MQ=255)                                                                                       ccTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAACACAATTGGGTTGGTAGt     >  2:960263/1‑97 (MQ=255)                                                                                        cTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAACACAATTGGGTTGGTAGTc    >  2:794112/1‑97 (MQ=255)                                                                                          tCTGTAATGTGAATTTTTAAAATTACAGTTTACATCTAACGCTGCGCAATATATTCTGTATATAGAAGTGTCACAACACAATTGGGTTGGTAGTccc  >  2:1005155/1‑97 (MQ=255)                                                                                             |                                                                                              GTTTAAAAGCATTATGCAATGCCAATCAACACTAATGGGGTGTAAGTATTTCCCTGTTAATATTTTATTAGCGTTATTTACATATACCTTCTGTAATGTGAATTTTTAAAATTACAGTTTACATGTAACGTTGTGCAATATATTCTGTATATAGAAGTGTAAAAACACAATTGGGTTGGTAGTCCC  >  BX571857/423832‑424017

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑