Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 589,875 C→A 8.0% P31T (CCT→ACT)  rpoC → DNA‑directed RNA polymerase subunit beta'

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE589,8750CA 8.0% 140.1 / 2.7 50P31T (CCT→ACT) rpoCDNA‑directed RNA polymerase subunit beta'
Reads supporting (aligned to +/- strand):  ref base C (23/23);  new base A (2/2);  total (25/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-01

CAAATCAATCAAATAGCACAGCTAATCTAAATTGAAGGAGGTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTTGTGGTAAATACAAACGTGTTCGCTACAAAGGCATGGTCTGTGACAGA  >  USA300TCH1516_ALE/589736‑590015
                                                                                                                                           |                                                                                                                                            
cAAATCAATCAAATAGCACAGCTAATCTAAATTGAAGGAGGTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAAcc                                                                                                                                             >  1:50188/1‑141 (MQ=255)
 aaaTCAATCAAATAGCACAGCTAATCTAAATTGAAGGAGGTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCt                                                                                                                                            <  1:250676/141‑1 (MQ=255)
   atcaatcaAATAGCACATATAATCAAAATTGAAGAAGGTAGGCTCATTAATTGATGTAAATAATTTCAATTATATGAAAATAGGATTGGCTACACCAAAAAAAATCCGTTCTTGGTCTTTTGCTGAAGTTAAAAAACCTGa                                                                                                                                          <  2:113492/141‑1 (MQ=255)
     caatcaaATAGCACAGCTAATCTAAATTGAAGGAGGTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGACTTTTGGTGAAGTTAAAAAACCTCaaa                                                                                                                                        >  2:363000/1‑141 (MQ=255)
      aatcaaATAGCACAGCTAATCTAAATTGAAGGAGGTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAAc                                                                                                                                       >  1:413505/1‑141 (MQ=255)
         caaATAGCACAGCTAATCTAAATTGAAGGAGGTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAAt                                                                                                                                    <  1:438438/141‑1 (MQ=255)
           aaTAGCACAGCTAATCTAAATTGAAGGAGGTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCa                                                                                                                                  >  2:167613/1‑141 (MQ=255)
                 acaGCTAATCTAAATTGAAAGAGGTAGGCTCCTTGAATGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCATTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCACCTccc                                                                                                                            >  2:294576/1‑141 (MQ=255)
                   aGCTAATATAAATTGAAGGAGGTAGGTTCCTTTATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTGACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGt                                                                                                                          <  2:248837/141‑1 (MQ=255)
                    gCTAATCTAAATTGAAGGAGGTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTa                                                                                                                         <  1:479690/141‑1 (MQ=255)
                     cTAATCTAAATTGAAGGAGGTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGTTCTTTTGGTGAAGTTAAAAAACCTGGAACAATCAACTACCGTAc                                                                                                                        >  1:350570/1‑141 (MQ=255)
                        aTCTAAATTGAAGGAGGTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAAACTGAAACAATCAACTACCGTACAtt                                                                                                                     >  2:417889/1‑141 (MQ=255)
                        aTCTAAATTGAAGGAGGTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAAACTGAAACAATCAACTACCGTACAtt                                                                                                                     >  2:166881/1‑141 (MQ=255)
                               ttGAAGGAGGTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCt                                                                                                              >  1:371284/1‑141 (MQ=255)
                                tGAAGGAGGTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTg                                                                                                             <  1:441553/141‑1 (MQ=255)
                                 gAAGGAGGTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGa                                                                                                            <  1:259013/141‑1 (MQ=255)
                                  aaGGAGTTAGGTACCTTGAGTGATGTTAATAATTTGCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTGTGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGaa                                                                                                           <  2:172128/141‑1 (MQ=255)
                                   aggaggTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGaaa                                                                                                          <  1:335205/141‑1 (MQ=255)
                                   aggaggTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGaaa                                                                                                          <  1:356427/141‑1 (MQ=255)
                                   aagaggTAGGGTTTTTAATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTTAACTGAAAAAATCCGTTCTTGATCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGaaa                                                                                                          <  2:459346/139‑1 (MQ=255)
                                           ggCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGt                                                                                                  <  2:190452/141‑1 (MQ=255)
                                                       gatGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTAAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGaa                                                                                      >  1:80190/1‑141 (MQ=255)
                                                        atGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGaaa                                                                                     <  1:234197/141‑1 (MQ=255)
                                                           tAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGaa                                                                                  <  1:335217/141‑1 (MQ=255)
                                                                aatTTCCATTATATGAAAATAGGATTGGCTACACCTGAAAAAATCAGTTCTTTGACTTTTGGTGAAGTTAAAAAACCTAAAACAATCAACTACCGTACATTAAAAACTGAAAACTAGAGGCTACTCTGTCAAAGAATTTTc                                                                             >  2:199461/1‑141 (MQ=255)
                                                                  tttCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCgg                                                                           >  1:476334/1‑141 (MQ=255)
                                                                     tcATTATATGAAAATAGTATTGGATTCAACTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGAcc                                                                        <  2:268582/140‑1 (MQ=255)
                                                                        ttATATGAAAATAGGATTGGCTTCAACTGAAAAAATCCGTTCTTGGTCTTTTGGAGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTAc                                                                     <  2:414127/141‑1 (MQ=255)
                                                                         tataTGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTAAATTAAAAACTGAAAAAGATGGTCTATTCTGCGAAAGAAATTTCGGACCTaaa                                                                    >  2:25820/1‑139 (MQ=255)
                                                                              gAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGTTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGa                                                               <  1:91630/141‑1 (MQ=255)
                                                                               aaaaTAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGAc                                                              >  1:265496/1‑141 (MQ=255)
                                                                                    aGGATTGGCTTCACCTGAAAACATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGa                                                         <  1:43547/141‑1 (MQ=255)
                                                                                    aGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTggcg                                                         >  1:1701/1‑139 (MQ=255)
                                                                                    aGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGa                                                         <  1:43327/141‑1 (MQ=255)
                                                                                     ggATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGTACCTACAAAAGACTGGGaa                                                        >  1:459238/1‑141 (MQ=255)
                                                                                           gCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGt                                                  <  1:400532/141‑1 (MQ=255)
                                                                                              tCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTtgt                                               >  1:402457/1‑141 (MQ=255)
                                                                                              tCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAAACTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTtgt                                               <  1:417889/141‑1 (MQ=255)
                                                                                              tCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAAACTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATAGTCAATTGTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTtgt                                               <  1:166881/141‑1 (MQ=255)
                                                                                                 ccTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTTGTGGt                                            >  1:33610/1‑141 (MQ=255)
                                                                                                  cTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTTGTGGTa                                           <  2:413505/141‑1 (MQ=255)
                                                                                                    gAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTTGTGGTaaa                                         >  2:339624/1‑141 (MQ=255)
                                                                                                      aaaaaTCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTGGTGGTAAATa                                       >  1:255317/1‑141 (MQ=255)
                                                                                                                   tGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTTGTGGTAAATACACACGTGTTCGc                          >  1:185153/1‑141 (MQ=255)
                                                                                                                   tGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTTGTGGTAAATACAAACGTGTTCGc                          >  2:197616/1‑141 (MQ=255)
                                                                                                                   tGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTTGTGGTAAATACAAACGTCTTCGc                          >  1:27226/1‑141 (MQ=255)
                                                                                                                           tGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTTGTGGTAAATACAAACGTGTTCGCTACAAAgg                  <  1:373184/141‑1 (MQ=255)
                                                                                                                             gTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGCAATGTAGTTGTGGTAAATACAAACGTGTTCGCTACAAAGGCa                >  2:386254/1‑141 (MQ=255)
                                                                                                                                     aaaaaaCCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTTGTGGTAAATACAAACGAGTTCGCTACAAAGGCATGGTCtgt        >  2:136701/1‑141 (MQ=255)
                                                                                                                                      aaaaaCCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTTGTGGTAAATACAAACGTGTTCGCTACAAAGGCATGGTCtgtg       >  1:67634/1‑141 (MQ=255)
                                                                                                                                        aaaCCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTTGTGGTAAATACAAACGTGTTCGCTACAAAGGCATGGTCTGTGAc     <  1:363000/141‑1 (MQ=255)
                                                                                                                                           ccTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTTGTGGTAAATACAAACGTGTTCGCTACAAAGGCATGGTCTGTGACAgg  >  1:225326/1‑140 (MQ=255)
                                                                                                                                           |                                                                                                                                            
CAAATCAATCAAATAGCACAGCTAATCTAAATTGAAGGAGGTAGGCTCCTTGATTGATGTAAATAATTTCCATTATATGAAAATAGGATTGGCTTCACCTGAAAAAATCCGTTCTTGGTCTTTTGGTGAAGTTAAAAAACCTGAAACAATCAACTACCGTACATTAAAACCTGAAAAAGATGGTCTATTCTGTGAAAGAATTTTCGGACCTACAAAAGACTGGGAATGTAGTTGTGGTAAATACAAACGTGTTCGCTACAAAGGCATGGTCTGTGACAGA  >  USA300TCH1516_ALE/589736‑590015

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: ‑