Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 93,268 G→A 76.9% A73T (GCT→ACT)  glpE → Thiosulfate sulfurtransferase GlpE

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE93,2680GA76.9% 61.8 / 20.7 39A73T (GCT→ACT) glpEThiosulfate sulfurtransferase GlpE
Reads supporting (aligned to +/- strand):  ref base G (3/6);  new base A (16/14);  total (19/20)
Fisher's exact test for biased strand distribution p-value = 4.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.15e-01

GAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTGCTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAG  >  USA300TCH1516_ALE/93140‑93400
                                                                                                                                |                                                                                                                                    
gAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGCACTAATGCTAGTa                                                                                                                          >  2:348166/1‑141 (MQ=255)
gAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAAACTGTAGAAGTGGTAACGGAAGAACGAATGCTATTa                                                                                                                          >  1:24654/1‑141 (MQ=255)
     gaagaGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTGCTAATGCTAGTAAatat                                                                                                                     <  1:341399/141‑1 (MQ=255)
     aaggaggagTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGGTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTCTTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAatat                                                                                                                     <  2:96219/138‑1 (MQ=255)
       agagGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTGCTAATGCTAGTAAATAttt                                                                                                                   <  1:215354/141‑1 (MQ=255)
           gagTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGcg                                                                                                               >  2:118170/1‑140 (MQ=255)
                         aCAAATCAATTGTTCCATACTTCATCCTGTTGATGAGATTGACTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATaa                                                                                                 <  2:18150/141‑1 (MQ=255)
                                aaTGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTAATAATGCTAGTAGATGTTTAGCTAAACAAGGTTATAACGTtata                                                                                          >  1:170170/1‑141 (MQ=255)
                                aaTGGTTCCATACTACATCCTGTTGATGAGATGGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGGAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTtata                                                                                          >  2:270310/1‑141 (MQ=255)
                                  tGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTAATAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATaaa                                                                                        >  2:237052/1‑141 (MQ=255)
                                     ttCCATACTTCATCCGGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCt                                                                                     <  2:272332/141‑1 (MQ=255)
                                          tACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTGGCTAAACAAGGTTATAACGTTATAAATCTTGAtg                                                                                >  1:168033/1‑141 (MQ=255)
                                                aTCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAACTATTGAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGtt                                                                          <  1:271826/141‑1 (MQ=255)
                                                   cTGTTGAAGAGATTGAGTTAATAAAAAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTtata                                                                       <  2:114168/141‑1 (MQ=255)
                                                     gTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTGCTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATaaa                                                                     <  1:330019/141‑1 (MQ=255)
                                                      ttGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTGCTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAg                                                                    >  2:206400/1‑141 (MQ=255)
                                                        gatgaGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGGAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCt                                                                  <  1:182119/141‑1 (MQ=255)
                                                          tgaGATTGAGTAAATAAAAAAAAAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTGCTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTa                                                                <  1:121323/141‑1 (MQ=255)
                                                             gaTTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTGCTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATga                                                             <  2:103484/141‑1 (MQ=255)
                                                              aTTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTGCTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATgaa                                                            <  1:333973/141‑1 (MQ=255)
                                                                 gAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAAAGTTATAAATCTTGATGGTGGTTATAAAGCTTATgaagaa                                                         >  2:225385/1‑141 (MQ=255)
                                                                        tCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACg                                                  >  2:19390/1‑141 (MQ=255)
                                                                               aGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTa                                           >  1:338875/1‑141 (MQ=255)
                                                                                    aaaaTAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATa                                      >  1:86882/1‑141 (MQ=255)
                                                                                          aaaCCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACaag                                >  1:59641/1‑141 (MQ=255)
                                                                                           aaCCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTGCTAATGCTAGTAAATATTTAGCTAAACAAGGTTATGACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTGATGATACACaaga                               >  2:131209/1‑141 (MQ=255)
                                                                                             ccTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAGGCTTATGAAGAAGAAAACGATAGTTATGATACACaagaag                             <  1:282250/141‑1 (MQ=255)
                                                                                             ccTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACaagaag                             <  1:380545/141‑1 (MQ=255)
                                                                                             ccTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACaagaag                             <  2:339971/141‑1 (MQ=255)
                                                                                             ccTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACaagaag                             <  1:86343/141‑1 (MQ=255)
                                                                                              cTATTATGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAagaaga                            <  1:200643/141‑1 (MQ=255)
                                                                                                tttatGTAATCTGTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAat                          <  1:5433/140‑1 (MQ=255)
                                                                                                atgtagTAATCTGTAGAAGTTGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAat                          <  2:153754/136‑1 (MQ=255)
                                                                                                            gTAGAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAg              <  2:21012/141‑1 (MQ=255)
                                                                                                              aGAAGTGGTAACAGAAGTGCTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGaa            >  2:165178/1‑141 (MQ=255)
                                                                                                               gAAGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGaaa           >  1:56793/1‑141 (MQ=255)
                                                                                                                 aGTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATAAAAAAGTATAGAAAtt         >  2:197413/1‑141 (MQ=255)
                                                                                                                  gTGGTAACAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTa        >  2:325944/1‑141 (MQ=255)
                                                                                                                        aCAGAAGTACTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAg  >  1:73537/1‑141 (MQ=255)
                                                                                                                                |                                                                                                                                    
GAACAGAAGAGGAGTATGCATTAGGACATATCAATGGTTCCATACTTCATCCTGTTGATGAGATTGAGTCATTCAATAAAGAAAAAAATAAAACCTATTATGTAATCTGTAGAAGTGGTAACAGAAGTGCTAATGCTAGTAAATATTTAGCTAAACAAGGTTATAACGTTATAAATCTTGATGGTGGTTATAAAGCTTATGAAGAAGAAAACGATAGTTATGATACACAAGAAGAATATAAAAGTATAGAAATTAAAGCAG  >  USA300TCH1516_ALE/93140‑93400

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: ‑