Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE602,4660GT25.0% 123.4 / 13.8 52intergenic (+56/‑104)hchA/araBMolecular chaperone Hsp31 and glyoxalase 3/Ribulokinase
Reads supporting (aligned to +/- strand):  ref base G (15/24);  new base T (13/0);  total (28/24)
Fisher's exact test for biased strand distribution p-value = 6.29e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AACAGGTGACAGTCCTTTAGCTTCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTGGAATTGATTATGGAACTGCT  >  USA300TCH1516_ALE/602329‑602605
                                                                                                                                          |                                                                                                                                           
aaCAGGTGACAGTCCTTTAGCTTCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCa                                                                                                                                          >  2:15811/1‑141 (MQ=255)
 aCAGGTGACAGTCCTTTAGCTTCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCaa                                                                                                                                         <  2:9817/141‑1 (MQ=255)
               tttAGCTTCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATAc                                                                                                                           <  2:395108/141‑1 (MQ=255)
                      tCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTaaa                                                                                                                    <  2:264353/141‑1 (MQ=255)
                       aaaaTGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTaaaa                                                                                                                   <  2:164535/140‑1 (MQ=255)
                             aGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAAc                                                                                                             <  2:397721/141‑1 (MQ=255)
                                       aTTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAg                                                                                                   <  2:287812/141‑1 (MQ=255)
                                           gCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATg                                                                                               >  1:33697/1‑141 (MQ=255)
                                              gTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGTCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGAtt                                                                                            >  2:67411/1‑141 (MQ=255)
                                                taataaAATGTTAAATACAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTa                                                                                          <  1:322198/141‑1 (MQ=255)
                                                    gAAATGTTAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTCTTTTTTTTTTTTCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGa                                                                                       >  2:150638/1‑141 (MQ=255)
                                                    gAAATGTTAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTCTTTTTTTTTTTGCAAAATTTAAGTGATACTTGTAAAATAGAAACTATTATGAGTATGATTTAAGa                                                                                       >  2:158148/1‑141 (MQ=255)
                                                        tGTTAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACg                                                                                  <  1:217205/141‑1 (MQ=255)
                                                          ttAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTTTTTTTTTTTAATTGATACTTGTAAAACAGAATCTATTATGAGTATGATTTAAGAAAActct                                                                                >  2:68468/1‑141 (MQ=255)
                                                          ttAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTTTCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCt                                                                                >  2:297205/1‑141 (MQ=255)
                                                          ttAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCt                                                                                >  2:384435/1‑141 (MQ=255)
                                                             aaTGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGc                                                                             >  1:97901/1‑141 (MQ=255)
                                                              aTGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCa                                                                            >  1:152334/1‑141 (MQ=255)
                                                                gCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCaaa                                                                          >  1:174879/1‑141 (MQ=255)
                                                                  aaTACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAAc                                                                        >  1:114353/1‑141 (MQ=255)
                                                                     aCAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑‑TTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACtaat                                                                    <  2:381477/141‑1 (MQ=255)
                                                                      cAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACtaat                                                                    <  2:350459/141‑1 (MQ=255)
                                                                      cAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACtaat                                                                    <  1:376146/141‑1 (MQ=255)
                                                                      cAAAAAAAATAATAAAATATTAATGAGAGGAGCCTCCTATGTAAATGTATGGGGGCAC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACtaat                                                                    <  1:34080/141‑1 (MQ=255)
                                                                      aaaaaaaaaTAATTAAATATTAAATAGAGGAGCCTCATATGTAAATGTATGAGGGCAC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACtaat                                                                    <  1:387261/140‑1 (MQ=255)
                                                                       aaaaTAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACtaata                                                                   <  2:338645/141‑1 (MQ=255)
                                                                       aaaaTAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACtaata                                                                   <  2:232417/141‑1 (MQ=255)
                                                                        aaataaatAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACTGTGGCAAAACtaataa                                                                  >  1:351034/1‑141 (MQ=255)
                                                                        aaataaatAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACtaataa                                                                  >  1:116901/1‑141 (MQ=255)
                                                                           taaataaTTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTTTTTTTTTTTAAGTGATACTTGTAAAATAGAATCTATTATGTTTATGATTTAAGAAAACGCTTGCATACCTAATAAcca                                                               >  2:66546/1‑140 (MQ=255)
                                                                           taaataaTTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTTTTTTTTTTTAAGTGATACTGGTAAAATAGAACCTATTTTTAGTATGAGTTAAGAAGACGCTTGCAAAACTAATAAACg                                                               >  2:86850/1‑141 (MQ=255)
                                                                           taaataaTTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCg                                                               >  1:160983/1‑141 (MQ=255)
                                                                              ataatTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTTTTTTTTTTTAAGTTATACATGTAAAATAGAACCTCTTAGTAGAATGTGTTAAGAAAACTCTTGCGAACCtaataaaccaaa                                                            >  2:424360/1‑135 (MQ=255)
                                                                                              taGAAGATCGTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTGGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATggagga                                            <  2:196858/141‑1 (MQ=255)
                                                                                                gaggagCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGaaa                                          <  2:257463/141‑1 (MQ=255)
                                                                                                   gagCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACat                                       <  2:406603/141‑1 (MQ=255)
                                                                                                   gagCCCCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACat                                       <  2:294283/141‑1 (MQ=255)
                                                                                                     gCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACatga                                     <  2:114353/141‑1 (MQ=255)
                                                                                                      ccTCATATGTAAATGTATGAGGGCTCTTTTTTTTTTTGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACatga                                     >  2:62612/1‑141 (MQ=255)
                                                                                                      ccTCATATGTAAATGTATGAGGGCTCTTTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACatga                                     >  1:347585/1‑141 (MQ=255)
                                                                                                         cATATGTAAATGTATGAGGGCTC‑TTTTTTTTTTTTTTTTTTTTATTGATACTTGGAAAATAGAACTTATTATGAGTATGTTTTAAGTAAACGCTTGCACAACTAATAACCGCAACTAGCGATATGGAGTAAAAATGATGTc                                 >  2:302128/1‑141 (MQ=255)
                                                                                                         cATATGTAAATGTATGAGGGCTC‑TTTTTTTTTTTTTTTTTTTAAGTGATACTTGTAAAATAGAACCTATTATGTGTATGATTTAAGAAAACGCTTGCTCAACTAATAACCGCAACTAGCGATATGGAGGTAACATGATGTc                                 >  2:421924/1‑141 (MQ=255)
                                                                                                              gTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTtata                            <  2:174879/141‑1 (MQ=255)
                                                                                                                  aTGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCAt                        >  1:342455/1‑141 (MQ=255)
                                                                                                                    gTATGAGGGCTC‑TTTTTTTGTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTg                      <  1:51643/141‑1 (MQ=255)
                                                                                                                     tATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATAATTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTgg                     <  2:227591/141‑1 (MQ=255)
                                                                                                                       tGAGGGCTC‑TTTTTTTTTTGTAAATTTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTTTTATAGCATTTGaa                   >  2:252082/1‑141 (MQ=255)
                                                                                                                        gAGGGCTC‑TTTTTTTTTTTTTTTTTTTAAAAGATACATGGAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGAAACTAGCGATATGGAGGATACATTATGTCTTATAGCATTGGAAt                  >  2:81188/1‑141 (MQ=255)
                                                                                                                         aGGGCTC‑TTTTTTTTTTTCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTCTGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTGGAAtt                 >  1:430396/1‑141 (MQ=255)
                                                                                                                         aGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATAATTTAAGAAAACTCTTGCTAAACTAATAACCGCAGCTAGCGATAGGGAGGAAACATGATGTCGTATAGCATTGGAAtt                 >  1:218153/1‑141 (MQ=255)
                                                                                                                                  ttttttttGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTGGAATTGATTATgg         >  1:274025/1‑141 (MQ=255)
                                                                                                                                         tGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTGGAATTGATTATGGAACTGCt  <  1:366318/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                           
AACAGGTGACAGTCCTTTAGCTTCAAATGAGTTAGGAAAATTAGCAGTTAATGAAATGTTAAATGCAATACAAAATAAATAATTAAATATTAATTAGAGGAGCCTCATATGTAAATGTATGAGGGCTC‑TTTTTTTTTGGCAAAATTTAAGTGATACTTGTAAAATAGAACCTATTATGAGTATGATTTAAGAAAACGCTTGCAAAACTAATAACCGCAACTAGCGATATGGAGGAAACATGATGTCTTATAGCATTGGAATTGATTATGGAACTGCT  >  USA300TCH1516_ALE/602329‑602605

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑