Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,797,772 G→C 100% R7G (CGC→GGC)  phoR ← Alkaline phosphatase synthesis sensor protein PhoR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,797,7720GC100.0% 105.7 / NA 32R7G (CGC→GGC) phoRAlkaline phosphatase synthesis sensor protein PhoR
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (15/17);  total (15/17)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTC  >  USA300TCH1516_ALE/1797642‑1797908
                                                                                                                                  |                                                                                                                                        
tatGATCTTGTCTTGTTTGCTAGGGCTTGTTCGTTTTTTTCTGATAAAACATATGTGATTGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATACCATTAAGCCGTGGTGaacc                                                                                                                                <  2:185860/141‑3 (MQ=255)
  tGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACtt                                                                                                                              >  2:216719/1‑141 (MQ=255)
         gCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCAtt                                                                                                                       <  1:54062/141‑1 (MQ=255)
         gCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCAtt                                                                                                                       <  1:272301/141‑1 (MQ=255)
               tttGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCtt                                                                                                                 <  1:19552/140‑1 (MQ=255)
                   cTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAgg                                                                                                             >  1:49100/1‑141 (MQ=255)
                              tCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTTTTCTTTCGGTCTTCCCCAtt                                                                                                  >  2:70853/1‑141 (MQ=255)
                               cGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAAttt                                                                                                 >  2:81684/1‑141 (MQ=255)
                                          gATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGc                                                                                      >  2:214709/1‑141 (MQ=255)
                                                     tgtgATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTGATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGACCAGtt                                                                           >  2:59654/1‑141 (MQ=255)
                                                           ggAAGCGTGAATAATAATGTCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTtaata                                                                     <  2:248664/141‑1 (MQ=255)
                                                           ggAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTtaata                                                                     <  1:81684/141‑1 (MQ=255)
                                                                   gAATAATAATGCCTGATGTAACAAAACTGGTAATTAAAATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATAGTTCTTTAGGTCTTTCCAACTTATAGCCTAAGCAACGCACAGTTTTAATAATTtgttg                                                             >  2:209132/1‑139 (MQ=255)
                                                                    attaatattTCCTACTGTTACATAAATGATTATTCATATATCTCTTAGCAATAACATGAAGCCTGGGTGAAACTTTATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGc                                                            <  2:219090/139‑1 (MQ=255)
                                                                    aataataatGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGc                                                            <  2:212333/141‑1 (MQ=255)
                                                                           atGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAg                                                     >  2:186732/1‑141 (MQ=255)
                                                                                 aaTGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAt                                               <  2:211553/141‑1 (MQ=255)
                                                                                    gTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAtctt                                            <  1:214709/141‑1 (MQ=255)
                                                                                     tAACAAACCTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTATGGAGTTGTGGCCTCTTAGGATTAtcttc                                           <  2:257097/141‑1 (MQ=255)
                                                                                       aCAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTa                                         >  2:240387/1‑141 (MQ=255)
                                                                                               gATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTAtct                                 <  1:114741/141‑1 (MQ=255)
                                                                                                    ttaatATACTGCTTATCAATAGCATTGTGACGTGGTGAAACTTCAGCATTGTTCTTTAGGTCTTTCATTTTTATAGCCTATGCCTCGCAGAGTTTTACTAAGTTGTGGCTTATTGGGTTTTTCATCTAATTTATCTATTaa                            >  2:155644/1‑141 (MQ=255)
                                                                                                     taatATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTaaa                           <  1:223585/141‑1 (MQ=255)
                                                                                                           aCTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTg                     >  1:260420/1‑141 (MQ=255)
                                                                                                             tGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGat                   <  1:210298/141‑1 (MQ=255)
                                                                                                                ttATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATg                <  1:216719/141‑1 (MQ=255)
                                                                                                                  aTCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTa              >  2:205212/1‑141 (MQ=255)
                                                                                                                     aaTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACAt           <  2:246414/141‑1 (MQ=255)
                                                                                                                      aTAACATTAAGCCGTGGTGAACCTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATc          <  2:120805/141‑1 (MQ=255)
                                                                                                                      aTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTACAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGAGTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATc          >  1:256017/1‑141 (MQ=255)
                                                                                                                         aCATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGCCTGATATGTACATcaac       >  1:112129/1‑141 (MQ=255)
                                                                                                                              aaGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTc  >  1:32458/1‑141 (MQ=255)
                                                                                                                                  |                                                                                                                                        
TATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTC  >  USA300TCH1516_ALE/1797642‑1797908

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: ‑