Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,077,013 T→C 9.8% Y86C (TAT→TGT)  USA300HOU_1933 ← hypothetical membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,077,0130TC 9.8% 112.8 / 4.6 41Y86C (TAT→TGT) USA300HOU_1933hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base T (11/26);  new base C (2/2);  total (13/28)
Fisher's exact test for biased strand distribution p-value = 5.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.76e-01

GCCAAATTTTTTCCATTACTAGATGCCTGCACAACAATCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAACCATTTTGCTGCAGCAAATACAGATCCATAGACAATAATATGTTTCGGGTTATCCATCGAA  >  CP000730/2076875‑2077150
                                                                                                                                          |                                                                                                                                         
gCCAAATTTTTTCCATTACTAGATGCCTGCACAACAATCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCatatat                                                                                                                                         >  1:629432/1‑141 (MQ=255)
 ccAAATTTTTTCCATTACTAGATGCCTGCACAACAATCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTATCTTTACTCAtatata                                                                                                                                        <  1:566583/141‑1 (MQ=255)
    aaTTTTTTCCATTACTAGATGCCTGCACAACAATCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAGACTGTTTTCGAAATAATGTATGCAACGCGTGTTTTAACTTTACTCATATATAGtt                                                                                                                                     >  2:416359/1‑141 (MQ=255)
    aaTTTTTTCCATTACTAGATCCCTGCACAACAATCAAAATCACACAATGAATTAATGCTAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCCTGTTTTAACTGTACTCATATATAGtt                                                                                                                                     >  1:459542/1‑141 (MQ=255)
         ataacATTACTATATGCCTGTACAACAATCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAAtt                                                                                                                                <  2:76855/137‑1 (MQ=255)
          ttCCATTACTAGATGCCTGCACAACAATCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTCTCCACCGCACGCCTGAACTTTACTCATATGTAGTTGAATTg                                                                                                                               >  1:287116/1‑141 (MQ=255)
              aTTACTAGATGCCTGCACAAAAATTAAAATCACTTAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTAcc                                                                                                                           <  1:14813/141‑1 (MQ=255)
              aTTACTAGATGCCTGAACAACAATCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTAcc                                                                                                                           <  1:455383/141‑1 (MQ=255)
                  cTAGATGCCTGCACAACAATCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTtgt                                                                                                                       <  1:176284/141‑1 (MQ=255)
                   tAGATGCCTGCACAACAATCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGGATTGTATCTtgtg                                                                                                                      <  2:618682/141‑1 (MQ=255)
                      aTGCCTGCACAACAATCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGaaa                                                                                                                   >  2:153156/1‑141 (MQ=255)
                           tGCACAACAATCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCa                                                                                                              <  2:737403/141‑1 (MQ=255)
                               caacaaTCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGACATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCAcgcg                                                                                                          >  1:456295/1‑141 (MQ=255)
                                 acaaTCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATACATAGTTGAATTGTACCTTGTGAAAAATCACGCGTa                                                                                                        >  1:740204/1‑141 (MQ=255)
                                 acaaTCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATACATAGTTGAATTGTACCTTGTGAAAAATCACGCGTa                                                                                                        >  1:740115/1‑141 (MQ=255)
                                  caaTCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTaa                                                                                                       <  1:26751/141‑1 (MQ=255)
                                  aaaTCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGACTTGTTTCTTGTGAAAAATCACGCGTaa                                                                                                       <  2:539022/140‑1 (MQ=255)
                                            cacaTAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTaac                                                                                             <  2:221155/141‑1 (MQ=255)
                                                    gAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACaacaaaca                                                                                     <  1:467839/141‑1 (MQ=255)
                                                    aaaTTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACaacaaaca                                                                                     <  1:478127/140‑1 (MQ=255)
                                                        tAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACAttca                                                                                 >  1:386696/1‑139 (MQ=255)
                                                        tAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATaaa                                                                                 <  2:129296/141‑1 (MQ=255)
                                                        tAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTaa                                                                                 <  2:709721/141‑1 (MQ=255)
                                                         aaTGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATACATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAAt                                                                                <  2:740115/141‑1 (MQ=255)
                                                         aaTGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATACATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAAt                                                                                <  2:740204/141‑1 (MQ=255)
                                                          aTGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACACACATTAATc                                                                               >  1:90032/1‑141 (MQ=255)
                                                                  aataTTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAGAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAattatt                                                                       >  1:59084/1‑141 (MQ=255)
                                                                  aataTTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAattatt                                                                       <  1:433309/141‑1 (MQ=255)
                                                                           aTTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAAc                                                              <  1:262954/141‑1 (MQ=255)
                                                                           aTTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAAc                                                              <  2:507230/141‑1 (MQ=255)
                                                                                     ttGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAACCATTTtgctg                                                    <  1:251576/141‑1 (MQ=255)
                                                                                      tGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAACCATTTtgctgc                                                   <  1:697239/141‑1 (MQ=255)
                                                                                                    aaaTAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAACCATTTCGCTGCAGCAAATACAGATc                                     <  1:416359/141‑1 (MQ=255)
                                                                                                         atGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAACCATTTTGCTGCAGCAAATACAGATCCATAg                                >  1:141141/1‑141 (MQ=255)
                                                                                                         atGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAACCATTTTGCTGCAGCAAATACAGATCCATAg                                <  1:184836/141‑1 (MQ=255)
                                                                                                           gTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAACCATTTTGCTGCAGCAAATAAAGATCCATAGAc                              >  1:738793/1‑141 (MQ=255)
                                                                                                              tCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAACCATTTTGCTGCAGCAAATACAGATCCATAGACaat                           <  1:446928/141‑1 (MQ=255)
                                                                                                                        tttttAACTTTACTCATGTATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAAGCCAATTATTAACAATAACCATTTTGCTGCAGCAAATACAGATCCATAGACGATGATATGTTTc                 <  2:658808/140‑1 (MQ=255)
                                                                                                                                  tACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAACCATTTTGCTGCAGCAAATACAGATCCATAGACAATAATATGTTTCGGGTTATCCa       <  2:418135/141‑1 (MQ=255)
                                                                                                                                  tACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAACCATTTTGCTGCAGCAAATACAGATCCATAGACAATAATAGGTTTCGGGTTATCCa       >  1:35746/1‑141 (MQ=255)
                                                                                                                                   aCTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAACCATTTTGCTGCAGCAAATACAGATCCATAGACAATAATATGTTTCGGGTTATCCAt      <  2:456295/141‑1 (MQ=255)
                                                                                                                                    cTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAACCATTTTGCTGCAGCAAATACAGATCCATAGACAATAATATGTTTCGGGTTATCCATc     <  1:723201/141‑1 (MQ=255)
                                                                                                                                    cTCATATATAGTTGAAATGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAACCATTTTGCTGCAGCAAATACAGATCCATAGACAATAATATGTTTCGGGTTATCCATc     <  1:135133/141‑1 (MQ=255)
                                                                                                                                       atatatAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAACCATTTTGCTGCAGCAAATACAGATCCATAGACAAAAATATGTTTCGGGTTATCCATCGaa  <  2:235357/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                         
GCCAAATTTTTTCCATTACTAGATGCCTGCACAACAATCAAAATCACATAATGAATTAATGCAAATAATATTGAAATTAAAATAATTGAAATTGTTTTCGAAATAATGTATCCAACGCGTGTTTTAACTTTACTCATATATAGTTGAATTGTACCTTGTGAAAAATCACGCGTAATTGTCTTAACAACAAACATTAATCCAATTATTAACAATAACCATTTTGCTGCAGCAAATACAGATCCATAGACAATAATATGTTTCGGGTTATCCATCGAA  >  CP000730/2076875‑2077150

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑