Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 2,999,330 G→A 100% intergenic (+138/‑234) yeeP → / → flu b1999; predicted GTP‑binding protein/antigen 43 (Ag43) phase‑variable biofilm formation autotransporter

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6062,999,3300G→A100.0% 376.7 110intergenic (+138/‑234)yeeP/flub1999; predicted GTP‑binding protein/antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand):  new base (69/40):  ref base (0/1):  total (69/41)

Only 100 of 135 total aligned reads displayed.

AATAGAATAAAACGATCGATAAAACAGGTATCGATCGTTGCTATCGATCGTTTATAGTGGTTAA  >  REL606/2999298‑2999361
                                |                               
aaTAGAATAAAACGATCGATAAAACAGGTatcaat                               >  1:225615/1‑35 (MQ=255)
aaTAGAATAAAACGATCGATAAAACAGGTatcaat                               <  1:14121642/35‑1 (MQ=255)
aaTAGAATAAAACGATCGATAAAACAGGTatcaat                               >  1:3586679/1‑35 (MQ=255)
aaTAGAATAAAACGATCGATAAAACAGGTatcaat                               <  1:684002/35‑1 (MQ=255)
aaTAGAATAAAACGATCGATAAAACAGGTatcaat                               <  1:414476/35‑1 (MQ=255)
 aTAGAATAAAACGATCGATAAAACAGTTatcaatc                              >  1:519794/1‑35 (MQ=25)
 aTAGAATAAAACGATCGATAAAACAGGTatcaatc                              <  1:9175527/35‑1 (MQ=255)
 aTAGAATAAAACGATCGATAAAACAGGTatcaatc                              >  1:5465955/1‑35 (MQ=255)
 aTAGAATAAAACGATCGATAAAACAGGTatcaatc                              >  1:11108878/1‑35 (MQ=255)
 aTAGAATAAAACGATCGATAAAACAGGTatcaatc                              >  1:19352148/1‑35 (MQ=255)
 aTAGAATAAAACGATCGATAAAACAGGTatcaatc                              <  1:17852995/35‑1 (MQ=255)
  tAGAATAAAACGATCGATAAAACAGGTatcaatcg                             >  1:15640915/1‑35 (MQ=255)
  tAGAATAAAACGATCGATAAAACAGGTatcaatcg                             >  1:8851144/1‑35 (MQ=255)
  tAGAATAAAACGATCGATAAAACAGGTatcaatcg                             <  1:19488712/35‑1 (MQ=255)
   aGAATAAAACGATCGATAAAACAGGTATCAATCGt                            >  1:4240122/1‑35 (MQ=255)
   aGAATAAAACGATCGATAAAACAGGTATCAATCGt                            >  1:2162656/1‑35 (MQ=255)
   aGAATAAAACGATCGATAAAACAGGTATCAATCGt                            >  1:3154310/1‑35 (MQ=255)
   aGAATAAAACGATCGATAAAACAGGTATCAATCGt                            >  1:10263235/1‑35 (MQ=255)
    gAATAAAACGATCGATAAAACAGGTATCAATCGtt                           >  1:17114292/1‑35 (MQ=255)
    gAATAAAACGATCGATAAAACAGGTATCAATCGtt                           >  1:19820410/1‑35 (MQ=255)
    gAATAAAACGATCGATAAAACAGGTATCAATCGtt                           >  1:14068839/1‑35 (MQ=255)
    gAATAAAACGATCGATAAAACAGGTATCAATCGtt                           >  1:5965035/1‑35 (MQ=255)
     aaTAAAACGATCGATAAAACAGGTATCAATCGTTg                          >  1:4572254/1‑35 (MQ=255)
     aaTAAAACGATCGATAAAACAGGTATCAATCGTTg                          <  1:161083/35‑1 (MQ=255)
     aaTAAAACGATCGATAAAACAGGTATCAATCGTTg                          <  1:15713698/35‑1 (MQ=255)
     aaTAAAACGATCGATAAAACAGGTATCAATCGTTg                          <  1:15485446/35‑1 (MQ=255)
      aTAAAACGATCGATAAAACAGGTATCAATCGTTGc                         >  1:8574412/1‑35 (MQ=255)
      aTAAAACGATCGATAAAACAGGTATCAATCGTTGc                         >  1:8850239/1‑35 (MQ=255)
       tAAAACGATCGATAAAACAGGTATCAATCGTTGCt                        <  1:5677993/35‑1 (MQ=255)
       tAAAACGATCGATAAAACAGGTATCAATCGTTGCt                        >  1:10026637/1‑35 (MQ=255)
         aaaCGATCGATAAAACAGGTATCAATCGTTGCTat                      >  1:2399810/1‑35 (MQ=255)
         aaaCGATCGATAAAACAGGTATCAATCGTTGCTat                      <  1:9553621/35‑1 (MQ=255)
         aaaCGATCGATAAAACAGGTATCAATCGTTGCTat                      >  1:8590931/1‑35 (MQ=255)
         aaaCGATCGATAAAACAGGTATCAATCGTTGCTat                      >  1:19286756/1‑35 (MQ=255)
         aaaCGATCGATAAAACAGGTATCAATAGTTGCTat                      <  1:12498046/35‑1 (MQ=37)
          aaCGATCGATAAAACAGGTATCGATCGTTGCTatc                     <  1:5026319/35‑1 (MQ=255)
          aaCGATCGATAAAACAGGTATCAATCGTTGCTatc                     >  1:2576456/1‑35 (MQ=255)
          aaCGATCGATAAAACAGGTATCAATCGTTGCTatc                     >  1:11761145/1‑35 (MQ=255)
          aaCGATCGATAAAACAGGTATCAATCGTTGCTatc                     <  1:4809809/35‑1 (MQ=255)
          aaCGATCGATAAAACAGGTATCAATCGTTGCTatc                     >  1:12704570/1‑35 (MQ=255)
          aaCGATCGATAAAACAGGTATCAATCGTTGCTatc                     <  1:16023912/35‑1 (MQ=255)
          aaCGATCGATAAAACAGGTATCAATCGTTGCTatc                     <  1:7918255/35‑1 (MQ=255)
           aCGATCGATAAAACAGGTATCAATCGTTGCTatcg                    <  1:4925478/35‑1 (MQ=255)
           aCGATCGATAAAACAGGTATCAATCGTTGCTatcg                    <  1:14517867/35‑1 (MQ=255)
            cgatcgatAAAACAGGTATCAATCGTTGCTatcga                   <  1:8034745/35‑1 (MQ=255)
            cgatcgatAAAACAGGTATCAATCGTTGCTatcga                   >  1:13169882/1‑35 (MQ=255)
            cgatcgatAAAACAGGTATCAATCGTTGCTatcga                   >  1:2149059/1‑35 (MQ=255)
            cgatcgatAAAACAGGTATCAATCGTTGCTatcga                   <  1:10663082/35‑1 (MQ=255)
             gatcgatAAAACAGGTATCAATCGTTGCTatcgat                  <  1:6833803/35‑1 (MQ=255)
             gatcgatAAAACAGGTATCAATCGTTGCTatcgat                  <  1:10447404/35‑1 (MQ=255)
             gatcgatAAAACAGGTATCAATCGTTGCTatcgat                  <  1:1953194/35‑1 (MQ=255)
             gatcgatAAAACAGGTATCAATCGTTGCTatcgat                  >  1:13212948/1‑35 (MQ=255)
             gatcgatAAAACAGGTATCAATCGTTGCTatcgat                  <  1:1800234/35‑1 (MQ=255)
             gatcgatAAAACAGGTATCAATCGTTGCTatcgat                  >  1:8320650/1‑35 (MQ=255)
             gatcgatAAAACAGGTATCAATCGTTGCTatcgat                  >  1:4671470/1‑35 (MQ=255)
              atcgatAAAACAGGTATCAATCGTTGCTatcgatc                 >  1:11144750/1‑35 (MQ=255)
              atcgatAAAACAGGTATCAATCGTTGCTatcgatc                 <  1:15069148/35‑1 (MQ=255)
               tcgatAAAACAGGTATCAATCGTTGCTatcgatcg                <  1:8369657/35‑1 (MQ=255)
               tcgatAAAACAGGTATCAATCGTTGCTatcgatcg                >  1:9863977/1‑35 (MQ=255)
               tcgatAAAACAGGTATCAATCGTTGCTatcgatcg                <  1:13352164/35‑1 (MQ=255)
               tcgatAAAACAGGTATCAATCGTTGCTatcgatcg                <  1:1647585/35‑1 (MQ=255)
               tcgatAAAACAGGTATCAATCGTTGCTatcgatcg                <  1:2189876/35‑1 (MQ=255)
                cgatAAAACAGGTATCAATCGTTGCTATCGATCGt               >  1:2236092/1‑35 (MQ=255)
                cgacAAAACAGGTATCAATCGTTGCTATCGATCGt               >  1:17370732/1‑35 (MQ=38)
                 gatAAAACAGGTATCAATCGTTGCTATCGATCGtt              >  1:10280314/1‑35 (MQ=255)
                 gatAAAACAGGTATCAATCGTTGCTATCGATCGtt              >  1:7491876/1‑35 (MQ=255)
                 gatAAAACAGGTATCAATCGTTGCTATCGATCGtt              >  1:16220407/1‑35 (MQ=255)
                 gatAAAACAGGTATCAATCGTTGCTATCGATCGtt              >  1:4740068/1‑35 (MQ=255)
                  atAAAACAGGTATCAATCGTTGCTATCGATCGttt             >  1:7156440/1‑35 (MQ=255)
                  atAAAACAGGTATCAATCGTTGCTATCGATCGttt             >  1:3310732/1‑35 (MQ=255)
                  atAAAACAGGTATCAATCGTTGCTATCGATCGttt             >  1:10702601/1‑35 (MQ=255)
                  atAAAACAGGTATCAATCGTTGCTATCGATCGttt             >  1:13006204/1‑35 (MQ=255)
                   tAAAACAGGTATCAATCGTTGCTATCGATCGTTta            >  1:10430621/1‑35 (MQ=255)
                    aaaaCAGGTATCAATCGTTGCTATCGATCGTTtat           <  1:10469285/35‑1 (MQ=255)
                    aaaaCAGGTATCAATCGTTGCTATCGATCGTTtat           >  1:5225200/1‑35 (MQ=255)
                    aaaaCAGGTATCAATCGTTGCTATCGATCGTTtat           >  1:12540413/1‑35 (MQ=255)
                    aaaaCAGGTATCAATCGTTGCTATCGATCGTTtat           >  1:13235936/1‑35 (MQ=255)
                     aaaCAGGTATCAATCGTTGCTATCGATCGTTtata          >  1:12157797/1‑35 (MQ=255)
                     aaaCAGGTATCAATCGTTGCTATCGATCGTTtata          <  1:1454985/35‑1 (MQ=255)
                      aaCAGGTATCAATCGTTGCTATCGATCGTTTATAg         >  1:12315451/1‑35 (MQ=255)
                       aCAGGTATCAATCGTTGCTATCGATCGTTTATAGt        >  1:1060681/1‑35 (MQ=255)
                       aCAGGTATCAATCGTTGCTATCGATCGTTTATAGt        >  1:588136/1‑35 (MQ=255)
                       aCAGGTATCAATCGTTGCTATCGATCGTTTATAGt        >  1:16062808/1‑35 (MQ=255)
                       aCAGGTATCAATCGTTGCTATCGATCGTTTATAGt        >  1:1895699/1‑35 (MQ=255)
                        cAGGTATCAATCGTTGCTATCGATCGTTTATAGTg       >  1:18638765/1‑35 (MQ=255)
                         aGGTATCAATCGTTGCTATCGATCGTTTATAGTgg      >  1:1221573/1‑35 (MQ=255)
                         aGGTATCAATCGTTGCTATCGATCGTTTATAGTgg      >  1:5608503/1‑35 (MQ=255)
                         aGGTATCAATCGTTGCTATCGATCGTTTATAGTgg      <  1:5291689/35‑1 (MQ=255)
                         aGGTATCAATCGTTGCTATCGATCGTTTATAGTgg      >  1:4036781/1‑35 (MQ=255)
                         aGGTATCAATCGTTGCTATCGATCGTTTATAGGgg      >  1:19546193/1‑35 (MQ=37)
                          ggTATCAATCGTTGCTATCGATCGTTTATAGTGGt     <  1:17158003/35‑1 (MQ=255)
                          ggTATCAATCGTTGCTATCGATCGTTTATAGTGGt     >  1:17570240/1‑35 (MQ=255)
                           gTATCAATCGTTGCTATCGATCGTTTATAGTGGtt    >  1:16202899/1‑35 (MQ=255)
                           gTATCAATCGTTGCTATCGATCGTTTATAGTGGtt    <  1:3079170/35‑1 (MQ=255)
                           gTATCAATCGTTGCTATCGATCGTTTATAGTGGtt    <  1:2642967/35‑1 (MQ=255)
                            tATCAATCGTTGCTATCGATCGTTTATAGTGGTTa   >  1:3568134/1‑35 (MQ=255)
                            tATCAATCGTTGCTATCGATAGTTTATAGTGGTTa   <  1:8571290/35‑1 (MQ=255)
                             atcaatcgTTGCTATCGATCGTTTATAGTGGTTaa  <  1:13854712/35‑1 (MQ=255)
                             atcaatcgTTGCTATCGATCGTTTATAGTGGTTaa  >  1:6688629/1‑35 (MQ=255)
                             atcaatcgTTGCTATCGATCGTTTATAGTGGTTaa  >  1:2806342/1‑35 (MQ=255)
                                |                               
AATAGAATAAAACGATCGATAAAACAGGTATCGATCGTTGCTATCGATCGTTTATAGTGGTTAA  >  REL606/2999298‑2999361

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: 
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.