Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,505,544	C→A	15.1%	E54* (GAA→TAA)	yhfZ ←	putative DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,505,544	0	C	A	15.1%	119.2 / 3.3	39	E54* (GAA→TAA)	yhfZ	putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (14/19);  new base A (3/3);  total (17/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.28e-01

GCATAGTAAAAAGGAATGCCATCAAACTGGGCTTTCAATCCGCTCGCCAGGCCTTCGTACAAACGGGTATAGGGCAAGGGCATTGCACATACCACGTTGTTGATATCCACATGAGTCAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATCGATTACCGCACTTTTCACCCAACAAATAACGGGCCAGCGTCGTGATGACGACGCCTTCTTTTTTGATAAACGTTCGACGCATAATAAATTTTCAGTAAATTGAATATTTATATCTTCAGGAATTTGAAGATAAGGCGCA  >  CP009273/3505348‑3505760                                                                                                                                                                                                     |                                                                                                                                                                                                                         gcATAGTAAAAAGGAAGTCAATCAAACTGGTCGTTCAATCCGCTCGCCAGGCCTTCGTACAAACGGGTATAGGGCAAGGGCATTGCACATACCACGTTGTTGATATCCACATGAGTCAGCAATGCTTTGTTATCCATCGCGACCAGATAACTGCCATTGAGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATc                                                                                                                                             <  1:412436/274‑1 (MQ=255)                     agcAAACTGGGCTTTCAATCCGCTCGCCAGGCCTTCGTAAAAACGGGTATAGGGCAAGGGCATTGCACATACCACGTTGTTGATATCCACATGAGTCAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGc                                                                                                                                                                    <  1:43019/229‑1 (MQ=255)                                                 aGGCCTTCGTACAAACGGGTATAGGGCAATGGCATTGCACATACCACGTTGTTGATATCCACATGAGTCAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGtt                                                                                                                                                    <  1:215641/219‑1 (MQ=255)                                                        cGTACAAACGGGTATAGGGCAAGGGCATTGCACATACCACGTTGTTGATATCCACATGAGTCAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATAGCTCCGCTTGATTACAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAAt                                                                                                                                              >  2:45148/1‑218 (MQ=255)                                                            cAAACGGGTATAGGGCAAGGGCATTGCACATACCACGTTGTTGATATCCACATGAGTCAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATAGCTCCGCTTGATTACAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATCGAt                                                                                                                                          <  1:45148/218‑1 (MQ=255)                                                                              gggcaTTGCACATACCACGTTGTTGATATCCACATGAGTAAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTACAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGa                                                                                                                                                                                      >  1:73575/1‑156 (MQ=255)                                                                                  aTTGCACATACCACGTTGTTGATATCCACATGAGTAAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTACAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGaa                                                                                                                                                                                  <  2:73575/156‑1 (MQ=255)                                                                                           aCCACGTTGTTGATATCCACATGAGTCAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTc                                                                                                                                                                                                                >  2:531991/1‑117 (MQ=255)                                                                                           aCCACGTTGTTGATATCCACATGAGTCAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAAcgc                                                                                                                                                                                                           >  2:597415/1‑122 (MQ=255)                                                                                               cGTTGTTGATATCCACATGAGTCAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAAcg                                                                                                                                                                                                            <  1:532002/117‑1 (MQ=255)                                                                                               cGTTGTTGATATCCACATGAGTCAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGcc                                                                                                                                                                                                       <  1:597426/122‑1 (MQ=255)                                                                                                gttgttGATATCCACATGAGTCAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTGGATTCCCGCGTTTTCAACGCGGCCTGCGTCATGCCAACGGATGCACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATCGATTACCGCACTTTTCACCCAACCAATACCTGGCCAGCGTCGTGCGGACAACGCATTCTTTTTTGATAAACTTTCCAAGCCNCATCAATTTTCata                                             >  2:503223/1‑273 (MQ=255)                                                                                                        tttCCCCATGAGTCAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGANTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATCGATTACCGCACTTTTCACCCAACAAATAACGGGCCAGCGTCGTGATGACGACGCCTTCTTTTTTGATAAACGTTCGACGCATAATAAATTTTCAGTAAATTGaa                                     <  1:503233/273‑1 (MQ=255)                                                                                                              caTGAGTCAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTACAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATCGATTACCGCACTTTTCACCCAACAAATAACGGGCCAGCGTCGTGATGACGACGCCTTCTTTTTTGATAAACGTTCGACGCATAATAAATTTTCAGTAAATTGAATATTta                               >  2:7006/1‑275 (MQ=255)                                                                                                                  aGTCAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTACAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATCGATTACCGCACTTTTCACCCAACAAATAACGGGCCAGCGTCGTGATGACGACGCCTTCTTTTTTGATAAACGTTCGACGCATAATAAATTTTCAGTAAATTGAATATTtat                              <  1:7006/272‑1 (MQ=255)                                                                                                                    tCAGCAATGCATTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCt                                                                                                                                                                                                      >  1:639945/1‑102 (MQ=255)                                                                                                                        cAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGt                                                                                                                                                                                                  <  2:639934/102‑1 (MQ=255)                                                                                                                           tGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTg                                                                                                                                                                     >  2:615899/1‑128 (MQ=255)                                                                                                                             cTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTg                                                                                                                                                                     >  1:165244/1‑126 (MQ=255)                                                                                                                               ttGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAg                                                                                                                                                                 <  1:615910/128‑1 (MQ=255)                                                                                                                                 gTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAg                                                                                                                                                                 <  2:165241/126‑1 (MQ=255)                                                                                                                                       cATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTg                                                                                                                                                                     >  2:307452/1‑116 (MQ=255)                                                                                                                                           tcGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAg                                                                                                                                                                 <  1:307457/116‑1 (MQ=255)                                                                                                                                            cgcccAGATAACTGCCATTGCGCCCACGGTGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATCGATTACCGCACTTTTCACCCAACAAATAACGGGCCAGCGTCGTGATGACGACGCCTTCTTTTTTGATAAACGTTCGACGCATAATAAATTTTCAGTAAATTGAATATTTATATCTTCAGGAATTTGAAGATAAGGCGCa  <  1:425256/271‑1 (MQ=255)                                                                                                                                            cGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATCGAt                                                                                                                                          >  1:217851/1‑138 (MQ=255)                                                                                                                                                cAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATCGATTAcc                                                                                                                                      <  2:217847/138‑1 (MQ=255)                                                                                                                                                          ccATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATCGATTACCGCACTTTTCACCcaacaa                                                                                                                    >  1:589307/1‑146 (MQ=255)                                                                                                                                                             ttGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGaa                                                                                                                                                                                  >  1:348710/1‑81 (MQ=255)                                                                                                                                                             ttGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATCGATTACCGCACtttt                                                                                                                              >  1:303050/1‑133 (MQ=255)                                                                                                                                                              tGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATCGATTACCGCACTTTTCACCCAACAAATaa                                                                                                                <  2:589296/146‑1 (MQ=255)                                                                                                                                                                 gcCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGc                                                                                                                                                                              <  2:348705/81‑1 (MQ=255)                                                                                                                                                                 gcCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATCGATTACCGCACTTTTCAcc                                                                                                                          <  2:303045/133‑1 (MQ=255)                                                                                                                                                                    cACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCa                                                                                                                                                                                                                        <  1:331867/36‑1 (MQ=255)                                                                                                                                                                                        gCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTc                                                                                                                                                 >  2:266760/1‑87 (MQ=255)                                                                                                                                                                                          tCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTg                                                                                                                                                                     >  1:244441/1‑65 (MQ=255)                                                                                                                                                                                            cGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACgg                                                                                                                                                                               >  1:623658/1‑53 (MQ=255)                                                                                                                                                                                            cGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATc                                                                                                                                             <  1:266764/87‑1 (MQ=255)                                                                                                                                                                                              cTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAg                                                                                                                                                                 <  2:244437/65‑1 (MQ=255)                                                                                                                                                                                                tGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGcatt                                                                                                                                                                           <  2:623647/53‑1 (MQ=255)                                                                                                                                                                                                     |                                                                                                                                                                                                                         GCATAGTAAAAAGGAATGCCATCAAACTGGGCTTTCAATCCGCTCGCCAGGCCTTCGTACAAACGGGTATAGGGCAAGGGCATTGCACATACCACGTTGTTGATATCCACATGAGTCAGCAATGCTTTGTTATCCATCTCGACCAGATAACTGCCATTGCGCCCACGGCGTTCAATCCGTATCGCTCCGCTTGATTCCAGCGTTTTCAACGCGGCCTGCGTCAGGCCAACGGATGAACGGCATTCATTTGCCAGCTCATCTATGGTTTTCAATCGATTACCGCACTTTTCACCCAACAAATAACGGGCCAGCGTCGTGATGACGACGCCTTCTTTTTTGATAAACGTTCGACGCATAATAAATTTTCAGTAAATTGAATATTTATATCTTCAGGAATTTGAAGATAAGGCGCA  >  CP009273/3505348‑3505760

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑