Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	U00096	1,708,751	0	A	G	30.2%	64.4 / 32.5	55	E611E (GAA→GAG)	rsxC	SoxR [2Fe‑2S] reducing system protein RsxC
Reads supporting (aligned to +/- strand):  ref base A (14/23);  new base G (12/4);  total (26/29)
Fisher's exact test for biased strand distribution p-value = 1.77e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTA  >  U00096/1708603‑1708893                                                                                                                                                     |                                                                                                                                               cTATCGCCCGCGCCTAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGCCGATCCTCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGaa                                                                                                                                                <  1:1268824/149‑1 (MQ=255)      gCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGCCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCaga                                                                                                                                           <  2:1268825/149‑1 (MQ=255)              ctaaGGGCGCAATCTGGAACATCTTCAGTCTATTGCGGACGCAGAACCACTGGGGGATCCGCGCAAAGCCGCCGTAGAAGCCGCTATTGCCCGTGACAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGTAACCAGAAGAACAgg                                                                                                                                   <  2:1268845/147‑1 (MQ=14)               tacagtggcAATCTGGCACATCTACAGGATACTTCGGAAGCAGCAACACAGGCCGATCCTCGTAAATCCGCCGTCGAAGCAGCTATAGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGt                                                                                                                                  <  2:1268848/142‑1 (MQ=9)               aaaGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAATCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGt                                                                                                                                  <  2:1268828/149‑1 (MQ=255)                aaGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGt                                                                                                                                  <  1:1268829/148‑1 (MQ=255)                  tcgcggAATCTGGAAGATCAACAGGCTAATCAGGAACCAGAAACAGAGGCCGATCCTCGAAAATCCGCCGTCGAAGCCGCTATAGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGa                                                                                                                               <  2:1268836/148‑1 (MQ=14)                    tcgcAATCTGGAACAGCATCAGGATAATGAGGAACCAGAACAAGTGGTCGATCCTCGCAAAGCCGCCGTCGAAGCAGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATc                                                                                                                             <  2:1268832/148‑1 (MQ=14)                    gcggAAGCTGGAACACCATCAGGATACTGCGGACCCAGAACCCGAGGCCGATCCGCGCAAAGCCGCCGTCGAAGCAGCTATCGCCCGAGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATc                                                                                                                             <  2:1268831/149‑1 (MQ=14)                       cAATCTGGAAGATCACCAGGAAAATGCGGACCCAGAACACCATGGTGATCCGCGTAAATCCGCCGTCGAAGCAGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAAGCTAATGCGGAACCAGAAGAACAGGTCGATCcgc                                                                                                                          <  2:1268841/149‑1 (MQ=14)                       cAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGGCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCcgc                                                                                                                          <  1:1268834/149‑1 (MQ=255)                                               tGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCAAGCTGGAACAGCAACAGGAGAAAGCAAAACCAGCAGAACAGGTAGATCAGCTCAAAGCGGCCGTCGAcgccgcaa                                                                                                  >  2:1268975/1‑147 (MQ=14)                                                               caGGTCGATCCTCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAATAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGc                                                                                  <  2:1268839/149‑1 (MQ=255)                                                                     gATCCGCGCAAAGCTGCCGTCGAAGCCGCTATCGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAgcc                                                                                                                  <  1:1268842/111‑1 (MQ=255)                                                                     gATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCagaaga                                                                                                                                        <  1:1487488/89‑1 (MQ=255)                                                                     gATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAgg                                                                                                                                   <  1:1268846/94‑1 (MQ=255)                                                                     gATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAAc                                                                                                                                               <  1:1268843/82‑1 (MQ=255)                                                                     gATCCGCGCAAAGCCGCCGTCGAAGCAGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATcc                                                                                                                            <  1:1268844/101‑1 (MQ=255)                                                                                    gccgTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTc                                                                                                                                 <  1:1268854/81‑1 (MQ=255)                                                                                    gccgTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGAt                                                                                                                              <  1:1268853/84‑1 (MQ=255)                                                                                    gccgTCGAAGCAGCTATTGCCCGGGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGc                                                                                                       <  1:1268851/107‑1 (MQ=255)                                                                                      cgTCGAAGCCGCTATAGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAgaagaa                                                                                                                                       <  1:1268855/73‑1 (MQ=255)                                                                                        tCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAACAGGt                                                                                                                                  >  1:1268930/1‑76 (MQ=255)                                                                                          gAAGCCGCTATTGCCCGTGCCAAAGCTCGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAg                                                                                                                    <  1:1268856/88‑1 (MQ=11)                                                                                          gAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAg                                                                                                                    >  2:1268856/1‑88 (MQ=255)                                                                                            aGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACCGGCTAATGCGGAGCCAGAAGAACAGGTAGATCCGCGCAAAgctg                                                                                                                 >  1:1268934/1‑87 (MQ=11)                                                                                               cGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACCGGCTAATGCGGAGCCaga                                                                                                                                           >  2:1268936/1‑60 (MQ=11)                                                                                               cGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAACa                                                                                                                                     >  1:1268937/1‑66 (MQ=255)                                                                                                gCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCTAGCCAGCTGGAACAGCAACACGCTACTGCCGa                                                 >  2:1268857/1‑149 (MQ=14)                                                                                                gCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGa                                                 <  1:1268858/149‑1 (MQ=255)                                                                                                   aTTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAACAGGTTGATCCGCGCAAAGCTGCCGTCGaa                                                                                                         <  1:1268859/90‑1 (MQ=11)                                                                                                   aTTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAACAGGTAGATCCGCGCAAAGCTGCCGTCGaa                                                                                                         >  2:1268859/1‑90 (MQ=11)                                                                                                     tGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAACAGGTAGATCCGCGCAAAGCCGCCGTCGAAGCGGCTATTGcac                                                                                            >  1:1268947/1‑99 (MQ=11)                                                                                                      gCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTAGATCCGCGCAAAGCAGCCGTCGAAGCCGCTATTg                                                                                               >  2:1268935/1‑97 (MQ=255)                                                                                                       cccGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAACAGGTCGATCCGCGCaag                                                                                                                     >  1:1269016/1‑73 (MQ=255)                                                                                                           tGCCAAAGCGCGCAAGCTGGAACAGCAACCGGCTAATGCGGAGCCaga                                                                                                                                           >  1:1268951/1‑48 (MQ=11)                                                                                                           tGCCAAAGCGCGCAAGCTGGAACAGCAACCGGCTAATGCGGAGCCaga                                                                                                                                           <  2:1268951/48‑1 (MQ=11)                                                                                                               aaaGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCACAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGc                                                                              <  1:1268862/105‑1 (MQ=25)                                                                                                                 aGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCa                                                                                 >  1:1268909/1‑100 (MQ=21)                                                                                                                  gcgcgcAAGCTGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAAc                                                                                                                                      >  1:1268863/1‑46 (MQ=255)                                                                                                                  gcgcgcAAGCTGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAAc                                                                                                                                      <  2:1268863/46‑1 (MQ=255)                                                                                                                      gcAAGCTGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAACAGGTCGATCCGCGCAAAgccgcc                                                                                                               >  1:1268911/1‑65 (MQ=25)                                                                                                                       cAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCTGCCGTCGAAGCGGCTATTGc                                                                                              >  1:1268958/1‑81 (MQ=255)                                                                                                                       cAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCAGCCGTCGAAg                                                                                                        >  1:1268964/1‑71 (MQ=21)                                                                                                                        aaGCTGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAACAg                                                                                                                                    >  2:1268962/1‑42 (MQ=255)                                                                                                                        aaGCTGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAACAGGt                                                                                                                                  <  1:1268953/44‑1 (MQ=255)                                                                                                                        aaGCTGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAACAGGt                                                                                                                                  >  2:1268953/1‑44 (MQ=255)                                                                                                                        aaGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGccgccg                                                                                                              >  1:1268899/1‑64 (MQ=35)                                                                                                                         aGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCAGCCGTCGAAGCCGCTATTGCACGAGCCAAAGCAc                                                                                >  2:1268959/1‑93 (MQ=255)                                                                                                                          gCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCAGCCGTCGAAGCGGCTAt                                                                                                 >  2:1268961/1‑75 (MQ=255)                                                                                                                           cTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTAGATCCGCGCAAAGcagccg                                                                                                              >  2:1268956/1‑61 (MQ=255)                                                                                                                                aCAGCAACAGGCTAATGCGGATTTTGTATAAATGTTCGTTCCGCGAATTGCCGCAGTAGAATTCGCTAATGCCCGTGCCTAAGAACGCAAGCTGGAACAGCAACAGGCTAATGCCGATCCAGAACAACAGGTCGATCCGCGCAAAgccg                 <  2:1268899/149‑1 (MQ=2)                                                                                                                                 cAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCACGTGCCAAAGACCGCAAGCTGGAGCAGCAACAGGGGAATGCAGAGCCAGAACAAAAGGTCTATCCGCGCAAAgccgc                >  2:1268869/1‑149 (MQ=11)                                                                                                                                       cAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGc                                                                                                       >  1:1268867/1‑56 (MQ=35)                                                                                                                                               tGCGGATCCAGAAGAACAGGTCGATCCGCGAAAAGCCGCCTTCGTAGCCGATATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTa  <  1:1268869/149‑1 (MQ=14)                                                                                                                                               tGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCGGTGCCAGAACAACAGGTAGATCCGCGCAAAGCCGCAGTCGACGCCGCTa  >  1:1268979/1‑149 (MQ=11)                                                                                                                                                    aaCCAGAAGAACAGGTCGATCCGCGCAAAGCTGCCGTCGaa                                                                                                         >  2:1268978/1‑41 (MQ=255)                                                                                                                                                     |                                                                                                                                               CTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAACAGGCTAATGCCGAGCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTA  >  U00096/1708603‑1708893

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑