Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	566,245	0	G	A	37.0%	58.1 / 50.0	54	pseudogene (132/279 nt)	exoD	pseudogene, DLP12 prophage, phage‑type exonuclease family,Phage or Prophage Related
Reads supporting (aligned to +/- strand):  ref base G (14/20);  new base A (11/9);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 4.02e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGG  >  NC_000913/566109‑566372                                                                                                                                         |                                                                                                                                gCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATgcg                                                                                                                               <  2:518168/139‑1 (MQ=255) gCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATgcg                                                                                                                               <  1:636239/139‑1 (MQ=255)     cccAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCggg                                                                                                                           <  2:235087/139‑1 (MQ=255)      ccAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGt                                                                                                                          <  1:92393/139‑1 (MQ=255)       cAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCGCGACATAATGTAGGCCTTCACGCTTCATGCGCGGGTc                                                                                                                         >  1:581729/1‑139 (MQ=255)             cAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGtt                                                                                                                   >  1:888023/1‑139 (MQ=255)                 aCCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCa                                                                                                               <  1:651599/139‑1 (MQ=255)                 aCCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCa                                                                                                               <  2:632584/139‑1 (MQ=255)                     aTTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGt                                                                                                           >  1:240214/1‑139 (MQ=255)                        tCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTAcc                                                                                                        <  2:729749/139‑1 (MQ=255)                                  ccTCGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATtttt                                                                                              <  2:240214/139‑1 (MQ=255)                                     cGTCCATTTTTTCGATGAACTCCGGCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTcg                                                                                           >  2:684041/1‑139 (MQ=255)                                             ttttCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCAATCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCACGCGCGGGTCAAAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCAccc                                                                                   <  2:581729/139‑1 (MQ=255)                                                tCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCcaca                                                                                <  2:844377/139‑1 (MQ=255)                                                  gATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATg                                                                              <  2:682906/139‑1 (MQ=255)                                                        cTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTGACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTAc                                                                        <  1:533260/139‑1 (MQ=255)                                                        cTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTAc                                                                        <  2:708878/139‑1 (MQ=255)                                                            ggCACGATCTCGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTGCCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCa                                                                    <  2:482837/139‑1 (MQ=255)                                                                     tcGTCAAAACTCGCCATGTACTTTTCATCCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCa                                                           <  1:856322/139‑1 (MQ=255)                                                                        tCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTAc                                                                        <  1:633849/123‑1 (MQ=255)                                                                        tCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTAc                                                                        >  2:633849/1‑123 (MQ=255)                                                                                            ttCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGt                                                                                        <  2:54609/87‑1 (MQ=255)                                                                                            ttCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGt                                                                                        >  1:54609/1‑87 (MQ=255)                                                                                               atcccGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGt                                                                                                                    >  2:678471/4‑56 (MQ=255)                                                                                               atcccGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGt                                                                                                                    <  1:678471/53‑1 (MQ=255)                                                                                                 tCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAacc                               >  2:186544/1‑139 (MQ=255)                                                                                                    gCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAaccacc                            >  1:251363/1‑139 (MQ=255)                                                                                                    gCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAaccacc                            >  1:321054/1‑139 (MQ=255)                                                                                                    gCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCcaca                                                                                >  1:470275/1‑87 (MQ=255)                                                                                                    gCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCcaca                                                                                <  2:470275/87‑1 (MQ=255)                                                                                                    gCTCAATCACGACATAATGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAaccacc                            >  2:479059/1‑139 (MQ=255)                                                                                                     cTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCAcc                                                                  >  2:491324/1‑100 (MQ=255)                                                                                                     cTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCAcc                                                                  <  1:491324/100‑1 (MQ=255)                                                                                                        aaTCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATGGTTGGCAAAGTAcc                                                                                                        >  1:647639/1‑59 (MQ=255)                                                                                                        aaTCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTAcc                                                                                                        <  2:647639/59‑1 (MQ=255)                                                                                                        aaTCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGc                        <  2:321054/139‑1 (MQ=255)                                                                                                              gACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCa                                                                                                               >  2:286203/1‑46 (MQ=255)                                                                                                              gACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCa                                                                                                               <  1:286203/46‑1 (MQ=255)                                                                                                                    aTGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCAccc                                                                                   >  1:585422/1‑68 (MQ=255)                                                                                                                    aTGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCAccc                                                                                   <  2:585422/68‑1 (MQ=255)                                                                                                                    aTGCAGGCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATg            >  2:201009/1‑139 (MQ=255)                                                                                                                          gCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCa                                                                                                   >  2:88862/1‑46 (MQ=255)                                                                                                                          gCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCa                                                                                                   <  1:88862/46‑1 (MQ=255)                                                                                                                          gCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATcc      >  1:869027/1‑139 (MQ=255)                                                                                                                          gCCTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATcc      >  1:127163/1‑139 (MQ=255)                                                                                                                           ccTTCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATccc     >  2:73785/1‑139 (MQ=255)                                                                                                                            cTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCCCGAAACCACCGAGCCGGAATTTCATGAAATCCCg    <  1:186544/139‑1 (MQ=255)                                                                                                                             ttCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCgg   <  2:251363/139‑1 (MQ=255)                                                                                                                             ttCACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCTGACTTTATGGCCTCGAAACCACCGAGCCGGAACTTCATGAAATCCCgg   >  2:477233/1‑139 (MQ=255)                                                                                                                              tCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCggg  <  2:888023/139‑1 (MQ=255)                                                                                                                               cACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGc                        <  2:135766/116‑1 (MQ=255)                                                                                                                               cACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGc                        >  1:135766/1‑116 (MQ=255)                                                                                                                               cACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATg                                                                              <  2:609841/62‑1 (MQ=255)                                                                                                                               cACGCTTCATACGCGGGTCATAGTTGGCAAAGTACCAGGCATTTTTTCGCGTCACCCACATg                                                                              >  1:609841/1‑62 (MQ=255)                                                                                                                                    ttCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTcgcg                                                                                         >  2:664396/1‑46 (MQ=255)                                                                                                                                    ttCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTcgcg                                                                                         <  1:664396/46‑1 (MQ=255)                                                                                                                                         |                                                                                                                                GCTCCCCAAATACAAAACCAATTTCAGCCAGTGCCTCGTCCATTTTTTCGATGAACTCCGGCACCATCTCGTCAAAACTCGCCATGTACTTTTCATTCCGCTCAATCACGACATAATGCAGGCCTTCACGCTTCATGCGCGGGTCATAGTTGGCAAAGTACCAGGCATCTTTTCGCGTCACCCACATGCTGTACTGCACCTGGGCCATGTAAGCCGATTTTATTGCCTCGAAACCACCGAGCCGGAATTTCATGAAATCCCGGG  >  NC_000913/566109‑566372

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: ‑