Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,815,145 C→T 10.2% D33N (GAT→AAT)  dnaE ← DNA polymerase III subunit alpha

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,815,1450CT10.2% 120.1 / 3.8 47D33N (GAT→AAT) dnaEDNA polymerase III subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (17/24);  new base T (2/3);  total (20/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACAACTGTTTCGACTGTATTTAATCCATTTGTCACATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGAATATTTAAATATGCCACCATGATTGAATGGCCCCTTTCTATTAGTTAAGTTTTGTGCGT  >  USA300TCH1516_ALE/1815006‑1815280
                                                                                                                                           |                                                                                                                                       
acaacTGTTTCGACTGTATTTACTCCATTTGTCACCTATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACCTGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATc                                                                                                                                         <  2:271623/140‑1 (MQ=255)
  aacTGTTTCGACTGTATTTAATCCATTTGTCACATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATaaa                                                                                                                                       >  2:405742/1‑140 (MQ=255)
   acTGTTTCGACTGTATTTAATCCATTTGTCATATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAAc                                                                                                                                      <  2:485162/140‑1 (MQ=255)
   acTGTTTCGACTATATTTGTTCGATTTGTCACATATATTGTGATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCAGAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAAc                                                                                                                                      <  2:474376/140‑1 (MQ=255)
    cTGTTTCGACTGTATTTAATCCATTTGTCACATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACa                                                                                                                                     <  1:214399/140‑1 (MQ=255)
       tttCGACTGTATTTAATCCATTTGTCACATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACAttt                                                                                                                                  <  1:39511/140‑1 (MQ=255)
           taCTGTATTTAATCCATTTGTCACATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAACATCAGACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAg                                                                                                                              <  1:394000/139‑1 (MQ=255)
           gACTGTATTTAATCCATTTGTCACATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAg                                                                                                                              >  2:701994/1‑140 (MQ=255)
                  tttAATCCATTTGCAAAAAAAATTGTGATACCAAAAAGCGGTTTAAGGTTATTGGCGATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGc                                                                                                                       <  1:106525/140‑1 (MQ=255)
                    tAATCCATTTGTCACATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCaa                                                                                                                     >  2:695501/1‑140 (MQ=255)
                      aTCCATTTGTCACATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGt                                                                                                                   >  1:665685/1‑140 (MQ=255)
                       tCCATTTGTCACATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGGAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATTAACATTTTCAGACACAGCAAGTc                                                                                                                  >  1:757999/1‑140 (MQ=255)
                       tCCATTTGTCACATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTc                                                                                                                  >  2:668519/1‑140 (MQ=255)
                       tCCATTTGTCACATATATTGTCATACAAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATTAACATTTTCAGACACAGCAAGTc                                                                                                                  >  1:187553/1‑140 (MQ=255)
                       tCCATTTGTCACATATATTGTCATACAAAAAATCGGTTTAATGTTAGTTGCTATACATGCGTCATAAAATTTAGGCAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATGAACATTTTCAGACACAGAAAGTc                                                                                                                  >  1:194628/1‑140 (MQ=255)
                           tttGTCACATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTAc                                                                                                              <  2:65682/140‑1 (MQ=255)
                           tttGTCACATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTAc                                                                                                              <  1:581740/140‑1 (MQ=255)
                             tGTCACATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACgg                                                                                                            <  2:21820/140‑1 (MQ=255)
                              gTCACATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGACAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGc                                                                                                           >  2:26659/1‑140 (MQ=255)
                                          gTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGCTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTAttgt                                                                                               >  2:253035/1‑138 (MQ=255)
                                             aTACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTCTCAGTTATGACAAATGCATCAACATTTTCAGACACAGCAAGTCTTCCGGCATCTTCTATTTTTaa                                                                                            >  2:607384/1‑140 (MQ=255)
                                              tACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAg                                                                                           <  2:408891/140‑1 (MQ=255)
                                              tACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAg                                                                                           <  2:384738/140‑1 (MQ=255)
                                                 cAAAAATCGGTTTAATGTTATTTGCTATACATGCGTCATAAAATTTAGGAAAACCATACAATACATTGGTGACAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCACCTTCTATTTTTAAGCtt                                                                                        >  2:706554/1‑140 (MQ=255)
                                                 cAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCtt                                                                                        >  2:208841/1‑140 (MQ=255)
                                                  aaaaaTCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATTGCAAGTGCATCAACATTTTCAGACACCGCAAGTCTTACGGCATCTTCTATTTTTAAGCATg                                                                                       >  2:426685/1‑140 (MQ=255)
                                                    aaaTCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGaa                                                                                     <  1:711253/140‑1 (MQ=255)
                                                        cGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAAGTTa                                                                                 >  1:641166/1‑140 (MQ=255)
                                                             tAATGTTATTTGCTATACATGAATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACaaa                                                                            <  2:364052/140‑1 (MQ=255)
                                                                           ataCATGCATCATAAAATTTAGGAAAACCCTACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATg                                                              <  1:208531/140‑1 (MQ=255)
                                                                           ataCATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATg                                                              <  1:259280/140‑1 (MQ=255)
                                                                           ataCATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATg                                                              <  1:328013/140‑1 (MQ=255)
                                                                                  catcatAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGAATAttt                                                       >  1:260303/1‑140 (MQ=255)
                                                                                     catAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATTAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGAATATTTaaa                                                    <  2:187553/140‑1 (MQ=255)
                                                                                     catAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATTAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGAATATTTaaa                                                    <  2:757999/140‑1 (MQ=255)
                                                                                     catAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGAATATTTaaa                                                    <  1:668519/140‑1 (MQ=255)
                                                                                     cacaaaaTTTAGCAAAACCATACAATCCATTGGTGTCAGTTAGGGCAACTGCATTAACATTTTCATACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGAATATTTaaa                                                    <  2:194628/137‑1 (MQ=255)
                                                                                           aTTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGAATATTTAAATATGcc                                              <  2:415029/140‑1 (MQ=255)
                                                                                           aTTGAGGATAACCATACGATACATGGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGAATATTTAAATATGcc                                              <  2:676100/140‑1 (MQ=255)
                                                                                                     aCCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGAATATTTAAATATGCCACCATGATTg                                    <  1:701994/140‑1 (MQ=255)
                                                                                                       cATCCAGTACAATGGTGTCAGTTATGGCACGTGCATCAACATTTTCAGACGCAGCAAGTCTTACTGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGAATATTTAAATATGCCACCATGATTGaa                                  <  2:89682/140‑1 (MQ=255)
                                                                                                        atacaatacaTTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCGTGAATTTAACAAATCATAAGCCGTATGAATATTTAAATATGCCACCATGATTGAAt                                 <  1:120093/140‑1 (MQ=255)
                                                                                                          acaatacaTTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGAATATTTAAATATGCCACCATGATTGAATgg                               <  2:570047/140‑1 (MQ=255)
                                                                                                             atacaTTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGAATATTTAAATATGCCACCATGATTGAATGGccc                            >  1:371501/1‑140 (MQ=255)
                                                                                                                       gttaGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGATTATTTAAATATGACACCATGATTGAATGGCTCCTTTCTAtca                  >  2:759732/4‑138 (MQ=255)
                                                                                                                         cAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGATTGAATTTAACAAATCATAAGCCGTATGAATATTTACATATGCCACCATGATTGAATCGCCACTTTCTAtcact                >  1:96678/1‑136 (MQ=255)
                                                                                                                          aGTTATGGCAAGTGCATCAACATTTTCAGACACTGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGAATATTTAAATATGCCACCATGATTGAATGGCCCCTTTCTATTAGtt               <  1:456942/140‑1 (MQ=255)
                                                                                                                              aTGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGAATATTTAAATATGCCACCATGATTGAATGGCCCCTTTCTATTAGTTAAGt           >  2:116768/1‑140 (MQ=255)
                                                                                                                                       gCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGACTTTAACAAATCATAAGCCGTATGACTATTTAAATATGCCACCATGATTGAATGGCCCCCTTCTATTCGTTAAGTCTTCTGCGt  >  1:12833/1‑140 (MQ=255)
                                                                                                                                           |                                                                                                                                       
ACAACTGTTTCGACTGTATTTAATCCATTTGTCACATATATTGTCATACCAAAAATCGGTTTAATGTTATTTGCTATACATGCATCATAAAATTTAGGAAAACCATACAATACATTGGTGTCAGTTATGGCAAGTGCATCAACATTTTCAGACACAGCAAGTCTTACGGCATCTTCTATTTTTAAGCTTGAATTTAACAAATCATAAGCCGTATGAATATTTAAATATGCCACCATGATTGAATGGCCCCTTTCTATTAGTTAAGTTTTGTGCGT  >  USA300TCH1516_ALE/1815006‑1815280

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑