Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,420,196	T→C	N16D (AAC→GAC)	racR ←	Rac prophage; putative DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,420,196	0	T	C	97.0%	212.5 / ‑2.0	66	N16D (AAC→GAC)	racR	Rac prophage; putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (0/2);  new base C (31/33);  total (31/35)
Fisher's exact test for biased strand distribution p-value = 4.94e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.32e-01

TTCTTAATCCAGTCATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTTAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATGCGCATTACATTAGGCAATCCCTACCCTTACTG  >  NC_000913/1420102‑1420292                                                                                               |                                                                                                 ttCTTAATTCAGTCATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATgg                                                                                             <  2:118017/100‑1 (MQ=255) ttCTTAATCCAGTCATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATgg                                                                                             <  2:568807/100‑1 (MQ=255)    ttAATCCAGTCATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCt                                                                                          >  1:467191/1‑100 (MQ=255)    ttAATCCAGTCATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGACTTGACCGATCCCGAGGCGATTTTTTTGTCAATGGCCt                                                                                          >  2:877833/1‑100 (MQ=255)     tAATCCAGTCATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTTTCAATGTCCTg                                                                                         >  2:176123/1‑100 (MQ=255)     tAATCCAGTCATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTg                                                                                         >  1:70814/1‑100 (MQ=255)      aaTCCAGTCATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGc                                                                                        >  2:681923/1‑100 (MQ=255)      aaTCCAGTCATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGc                                                                                        >  2:647544/1‑100 (MQ=255)       aTCCAGTCATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGct                                                                                       <  2:501604/100‑1 (MQ=255)       aTCCAGTCATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGct                                                                                       >  1:495802/1‑100 (MQ=255)        tgcAGTCATGAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGGTTTGCCGGATCCCGAGGCGATTTTTTTGTCAATGGCCTGctc                                                                                      <  2:924357/98‑1 (MQ=255)        tCCAGTCATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGctc                                                                                      >  2:155598/1‑100 (MQ=255)              cATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCTATGCGATTTTTTTGTCAATGGCCTGCTCTATCGc                                                                                <  2:87122/100‑1 (MQ=255)              cATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGc                                                                                >  2:802553/1‑100 (MQ=255)              cATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGc                                                                                >  2:26947/1‑100 (MQ=255)              cATAAATTGATGGTGGTTGGACTTTAAAGGGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATccc                                                                                <  1:880651/100‑3 (MQ=255)               aTAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCt                                                                               >  1:350410/1‑100 (MQ=255)                tAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTc                                                                              >  2:16023/1‑100 (MQ=255)                  aaTTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCgg                                                                            <  2:1146790/100‑1 (MQ=255)                    ttGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGcc                                                                          <  1:745214/100‑1 (MQ=255)                    ttGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGcc                                                                          >  1:398311/1‑100 (MQ=255)                        tggtggTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTTAATGGCCTGCTCTATCGCTCGGCCTAAg                                                                      <  2:716877/100‑1 (MQ=255)                        tggtggTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAg                                                                      <  1:1069377/100‑1 (MQ=255)                             gtTGGACTTTAAACTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCttt                                                                 >  1:875473/1‑100 (MQ=255)                              ttGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGACGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTa                                                                <  1:356054/100‑1 (MQ=255)                                ggACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTAcc                                                              >  1:986147/1‑100 (MQ=255)                                  aCTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCAc                                                            <  1:334054/100‑1 (MQ=255)                                  aCTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCAc                                                            >  1:1060866/1‑100 (MQ=255)                                   cTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACt                                                           >  1:563280/1‑100 (MQ=255)                                   cTTTAAACTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACt                                                           >  1:686361/1‑100 (MQ=255)                                    tttAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTa                                                          >  2:1161084/1‑100 (MQ=255)                                     ttAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTACGTCTTTACCCCTaa                                                         >  2:1263911/1‑100 (MQ=255)                                     ttAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTaa                                                         >  1:485735/1‑100 (MQ=255)                                      tAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAg                                                        >  1:829456/1‑100 (MQ=255)                                       aaaGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGc                                                       >  2:988871/1‑100 (MQ=255)                                       aaaGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGc                                                       <  2:102303/100‑1 (MQ=255)                                         aGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCAt                                                     >  1:1252575/1‑100 (MQ=255)                                            ggCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGc                                                  <  1:925182/100‑1 (MQ=255)                                             gCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCt                                                 <  2:1088223/100‑1 (MQ=255)                                              cGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCtt                                                >  1:1142070/1‑100 (MQ=255)                                              cGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCtt                                                >  2:124315/1‑100 (MQ=255)                                              cGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCtt                                                >  1:1253907/1‑100 (MQ=255)                                               gTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCAGTAAGCATTGCtca                                               <  1:883226/100‑3 (MQ=255)                                               gTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTa                                               <  1:922292/100‑1 (MQ=255)                                                 gatctcTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAat                                             <  2:469007/95‑1 (MQ=255)                                                 gCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAat                                             <  2:127099/100‑1 (MQ=255)                                                     ccTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATtc                                         <  2:825532/100‑1 (MQ=255)                                                      cTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAatagatc                                        >  1:469011/1‑96 (MQ=255)                                                        ccGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTcc                                      >  2:19841/1‑100 (MQ=255)                                                        ccGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCAGTGCTTAATATTCTcc                                      >  1:1284785/1‑100 (MQ=255)                                                            cTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTTATATTCTCCTagg                                  <  1:877839/100‑3 (MQ=255)                                                            cTTTGATTTGACGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATg                                  <  2:495798/100‑1 (MQ=255)                                                              ttgatttgaCGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATgcg                                <  2:398307/100‑1 (MQ=255)                                                                gatttgaCGGATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATGCGca                              <  2:74880/100‑1 (MQ=255)                                                                  tttgaCGGATCCCGATGCGATTTTTTTGTCAATGTCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTTCTAGGCGcatt                            <  2:686357/100‑1 (MQ=255)                                                                        ggATCCCGATGCGATTTTTTTGTTAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATGCGcattacatta                      <  1:663720/100‑1 (MQ=255)                                                                        ggATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATGCGcattacatta                      <  2:467187/100‑1 (MQ=255)                                                                        ggATCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATGCGcattacatta                      <  2:78576/100‑1 (MQ=255)                                                                         gATCCCGACGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATGCGCATTACATTAg                     >  1:973695/1‑100 (MQ=255)                                                                           tCCCGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATGCGCATTACATTAGGc                   <  1:65900/100‑1 (MQ=255)                                                                              cGATGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATGCGCATTACATTAGGCAAt                <  2:119831/100‑1 (MQ=255)                                                                                aTGCGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATGCGCATTACATTAGGCAATcc              <  2:1284774/100‑1 (MQ=255)                                                                                   cGATTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATGCGCATTACATTAGGCAATCCCTa           <  2:1037001/100‑1 (MQ=255)                                                                                     aTTTTTTTGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATGCGCATTACATTAGGCAATCCCTAcc         <  2:350407/100‑1 (MQ=255)                                                                                      tttttttGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATGCGCATTACATTAGGCAATCCCTAccc        <  1:825591/100‑1 (MQ=255)                                                                                            tGTCAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATGCGCATTACATTAGGCAATCCCTACCCTTACTg  <  1:155600/100‑1 (MQ=255)                                                                                               |                                                                                                 TTCTTAATCCAGTCATAAATTGATGGTGGTTGGACTTTAAAGTGGCGTGCGACCTCCGCCTTTGATTTGACGGATCCCGATGCGATTTTTTTGTTAATGGCCTGCTCTATCGCTCGGCCTAAGTCTTTACCACTAAGCATTGCTTAATATTCTCCTATGCGCATTACATTAGGCAATCCCTACCCTTACTG  >  NC_000913/1420102‑1420292

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: ‑