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% 133.3 / NA 38R7G (CGC→GGC) phoRAlkaline phosphatase synthesis sensor protein PhoR
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (18/20);  total (18/20)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TAAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAAC  >  USA300TCH1516_ALE/1797636‑1797903
                                                                                                                                        |                                                                                                                                   
aaaataTATGATCTTGCATCGGTTGCTAGAGCTTGTGCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATGAATATACTGCTTATCAATAACATTAAGCcgtgg                                                                                                                                 <  1:180690/140‑1 (MQ=255)
  aataTATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCgtggtg                                                                                                                               <  1:296426/141‑1 (MQ=255)
      aatGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAAc                                                                                                                           <  1:170760/140‑1 (MQ=255)
         gATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTtc                                                                                                                        >  1:436716/1‑141 (MQ=255)
            cTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATACTAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTtcatc                                                                                                                     >  2:60696/1‑141 (MQ=255)
             ttGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTtcatca                                                                                                                    >  1:275302/1‑141 (MQ=255)
             ttGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTtcatca                                                                                                                    <  1:303176/141‑1 (MQ=255)
                  tCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATCTGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACGTTAAGCCGTGGTGAAACTTCATCATCGtt                                                                                                               >  1:177021/1‑141 (MQ=255)
                     tttGCTAGGGCGTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCtt                                                                                                            <  2:65509/140‑1 (MQ=255)
                        gCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAg                                                                                                         <  2:336816/141‑1 (MQ=255)
                            gagCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCt                                                                                                     <  2:471556/141‑1 (MQ=255)
                              gCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTCCTTTCGGTCttt                                                                                                   >  1:56930/1‑141 (MQ=255)
                                  gTTCGTGTTTTTCTGATAAACACTATGGTATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCaa                                                                                               >  2:542714/1‑141 (MQ=255)
                                     cGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTTTTCTTTAGGTCTTTCCAAttt                                                                                            >  2:351790/1‑141 (MQ=255)
                                      gtgtTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTta                                                                                           >  2:155925/1‑141 (MQ=255)
                                                  tAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAACCTAAGCCa                                                                               >  2:297968/1‑141 (MQ=255)
                                                     aaCATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGc                                                                            >  2:188602/1‑141 (MQ=255)
                                                              gATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCGTAAGGCACGCACAGTTTta                                                                   <  1:308783/141‑1 (MQ=255)
                                                                 ggAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTtaata                                                                <  2:496684/141‑1 (MQ=255)
                                                                    aGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGt                                                             >  2:524941/1‑141 (MQ=255)
                                                                      cGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCCCAGTTTTAATAAGTtg                                                           >  1:214637/1‑141 (MQ=255)
                                                                        tGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTtgtg                                                         <  1:244607/141‑1 (MQ=255)
                                                                           ataataatGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGct                                                      <  2:559717/141‑1 (MQ=255)
                                                                           ataataatGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGct                                                      >  2:46152/1‑141 (MQ=255)
                                                                                     cTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGAtt                                            <  1:155925/141‑1 (MQ=255)
                                                                                       aaTGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTAACGCCATTCGATTTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAt                                          >  1:552370/1‑141 (MQ=255)
                                                                                             aCAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTGATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCCCAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTa                                    >  2:47525/1‑141 (MQ=255)
                                                                                              cAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTaa                                   <  1:337176/141‑1 (MQ=255)
                                                                                                     gATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTAtcc                            >  1:190856/1‑140 (MQ=255)
                                                                                                             atatACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTGTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAAta                    >  1:320383/1‑140 (MQ=255)
                                                                                                               ataCTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGAc                  >  1:27186/1‑141 (MQ=255)
                                                                                                                  cTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGa               <  1:452154/141‑1 (MQ=255)
                                                                                                                       tATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGt          <  2:201514/141‑1 (MQ=255)
                                                                                                                        aTCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTa         <  1:117575/141‑1 (MQ=255)
                                                                                                                        aTCAACAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTa         <  2:475668/141‑1 (MQ=255)
                                                                                                                          cAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACa       <  1:284561/141‑1 (MQ=255)
                                                                                                                           aaTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGAATAGTTTTAAAAGGTTGTGTCTTCTTAGGATTCTTGGCGAATTTATCTCTTAAATGACTGATATGTACAt      <  2:117892/141‑1 (MQ=255)
                                                                                                                              aaCATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATcaa   <  2:164032/141‑1 (MQ=255)
                                                                                                                               aCATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGTCCTTTGCAATTTATAGCCTAAGCCACGCACAGTTTTAATACGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATcaac  <  2:150675/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                   
TAAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAAC  >  USA300TCH1516_ALE/1797636‑1797903

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑