Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 111,512 A→G 26.9% S194S (TCA→TCG)  USA300HOU_RS00520 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE111,5120AG26.9% 85.3 / 31.5 57S194S (TCA→TCG) USA300HOU_RS00520putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base A (21/20);  new base G (4/11);  total (26/31)
Fisher's exact test for biased strand distribution p-value = 1.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

TCTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  USA300TCH1516_ALE/111372‑111652
                                                                                                                                            |                                                                                                                                            
tCTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCa                                                                                                                                              <  2:160734/141‑1 (MQ=255)
       aGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAat                                                                                                                                       <  2:58742/141‑1 (MQ=255)
           aGTTAAAGAAGAAAACATAAAAAAAGAAATCGCAAACTTTAAGATTTTTGCGCAATATAGCAATTTTAAAGACATAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                   >  1:309546/1‑141 (MQ=255)
           aGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCa                                                                                                                                   >  1:34920/1‑141 (MQ=255)
             ttAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAt                                                                                                                                 >  1:301969/1‑141 (MQ=255)
              tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAtt                                                                                                                                <  1:378983/141‑1 (MQ=255)
              tAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAACCCAGAGGTGCCGTGTTATTCAGCTCAATATCAAtt                                                                                                                                <  1:304835/141‑1 (MQ=255)
               aaaGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTa                                                                                                                               <  2:306430/141‑1 (MQ=255)
                aagaagAAAACATAAAAAAAGAAATCGAGCGCTTTAAGTTTTTTGCGCAATATAGCAATCTTAAAGATTTAAGGAATTATAAAGATGGAGATATATCATATAATCAAGAGGTGCCGAGTTATTCAGCTCAATATCAATTaa                                                                                                                              >  2:313074/1‑141 (MQ=21)
                aagaagAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTaa                                                                                                                              >  2:173589/1‑141 (MQ=255)
                aagaagAAAACATAAAAAAAGAAAGCGAAAACTTTAAGTTTTTTGCGAAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTaa                                                                                                                              <  2:93710/141‑1 (MQ=255)
                  aaagaaAACATAAAAAAAGAAATCAAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                                                            <  1:282774/140‑1 (MQ=255)
                    agaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTaa                                                                                                                          <  1:147993/141‑1 (MQ=255)
                     gaaAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGAAATTTTAAAGATTTAATGTATTATAAAGATGGAGATATATAATATAATACAGAGGTGCCGAGTTATTCAGCTAAATATACATTAaataat                                                                                                                         >  2:312351/1‑141 (MQ=18)
                      aaaaCATAAAAAAAGAAATCTAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTGAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatg                                                                                                                        <  1:344260/141‑1 (MQ=255)
                         aCATAGAAAAAGAAAGCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                                                                     <  1:125779/141‑1 (MQ=255)
                         aCATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgatg                                                                                                                     <  1:329064/141‑1 (MQ=255)
                              aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                                                                >  2:231240/1‑141 (MQ=255)
                              aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                                                                <  1:71161/141‑1 (MQ=255)
                              aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                                                                >  1:260432/1‑141 (MQ=255)
                              aaaaaaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATtat                                                                                                                <  2:200214/141‑1 (MQ=255)
                                  aaGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATg                                                                                                            <  1:290397/141‑1 (MQ=255)
                                     aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTACCTAATGATTTTTATTATGTaa                                                                                                         >  2:99875/1‑141 (MQ=255)
                                     aaaTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTAAATTATTTATAAAGATGGAGATATATCATATAATCCATAGTTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTaa                                                                                                         <  2:67453/141‑1 (MQ=18)
                                       aTCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATATaaaa                                                                                                       >  2:347718/1‑141 (MQ=255)
                                        tCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTAGGCTCAATATCAATTAACTAATGATGATTATATTGTAAAAc                                                                                                      >  2:228396/1‑141 (MQ=255)
                                         cGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGACATATATCATATAATAAAAAGGTGACGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAcaca                                                                                                     >  2:309736/1‑141 (MQ=21)
                                         agAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACa                                                                                                     <  2:95495/140‑1 (MQ=255)
                                          gAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCGGAGATTATCTGTAAAATATCAATTAACTACTGATGATTATAATTTAaaaaaa                                                                                                    >  2:185333/1‑141 (MQ=18)
                                             aaCTTTAAGTTTTTTGGGAAAGATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                                 <  2:74553/141‑1 (MQ=17)
                                             aaCTTTAAGTATTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTa                                                                                                 <  2:168284/141‑1 (MQ=255)
                                               cTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGGTATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                               <  2:355158/141‑1 (MQ=255)
                                               cTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACg                                                                                               <  1:341568/141‑1 (MQ=255)
                                                  tAAGTTTTTTGCGCAATATAGCAATTTTAAAGATGTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTaa                                                                                            <  2:67369/141‑1 (MQ=255)
                                                                 atatAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAAGTAACTAATGAGGATGATAATGTAAGACAATTACGTAAAAGATATGACATAcc                                                                             >  1:81495/1‑141 (MQ=255)
                                                                      gCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATAccgacga                                                                        <  1:9226/141‑6 (MQ=11)
                                                                             tAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAgc                                                                 >  2:276897/1‑141 (MQ=255)
                                                                                 gATTTAATGAGTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCg                                                             <  2:139685/141‑1 (MQ=255)
                                                                                  aTTTAATGATTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGa                                                            <  2:198392/141‑1 (MQ=255)
                                                                                       gtatgttATAAAGATGGAGATATATCATATAATCCAGAGGTGCAGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATCACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                       <  2:81495/136‑1 (MQ=255)
                                                                                       aagAAGTATAAAGATGTAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                       <  2:263433/139‑1 (MQ=255)
                                                                                       aTGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtg                                                       >  1:363348/1‑141 (MQ=255)
                                                                                           atgataAAGATGGAGATACATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCtgttgt                                                   <  1:200423/138‑1 (MQ=255)
                                                                                                   gATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATCACGTAAAAGTTATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGt                                           <  2:227818/141‑1 (MQ=255)
                                                                                                   gATGGAGAGATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGt                                           <  2:186220/141‑1 (MQ=255)
                                                                                                           tatatCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAgtgca                                   >  1:3921/1‑137 (MQ=255)
                                                                                                                     aaTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGGATTTAAAAGGt                         >  1:276828/1‑141 (MQ=255)
                                                                                                                      aTCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGtt                        <  2:301969/141‑1 (MQ=255)
                                                                                                                       tCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGCTACAGGGAATTTAAAAGGTtc                       >  2:300839/1‑141 (MQ=255)
                                                                                                                        ccAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGAAATAACAACAAATAAAGCGCCGCAGCTGTTGTTGAAAGGTACAGGGAATTTAAACGGTtcc                      >  2:6243/1‑140 (MQ=255)
                                                                                                                          agagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatc                    <  1:10089/141‑1 (MQ=255)
                                                                                                                          agagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAAGAAATTTAAAAGCTtcatc                    >  2:347297/1‑141 (MQ=255)
                                                                                                                          acagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatc                    <  1:313074/139‑1 (MQ=255)
                                                                                                                           gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTtcatca                   >  1:329680/1‑141 (MQ=255)
                                                                                                                           gagGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCACAGAAACTGTTGTAGAAAGCTACAGGGAAATAAAAACGCtcataa                   >  2:391256/1‑139 (MQ=14)
                                                                                                                             ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGt                 >  1:7550/1‑141 (MQ=255)
                                                                                                                             ggTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGATGTTGAAAGGTACAGGGCATTTAAACGGTTCATCAgc                 >  2:272234/1‑140 (MQ=255)
                                                                                                                              gTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGtt                >  1:291332/1‑141 (MQ=255)
                                                                                                                                            aGCTCAATATCAATTAACTAAAGATGATTATCATGTAAAACAATTACATAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAt  >  2:61655/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                            
TCTACTGAGGAAGTTAAAGAAGAAAACATAAAAAAAGAAATCGAAAACTTTAAGTTTTTTGCGCAATATAGCAATTTTAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCAGCTCAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGTAAAAGATATGACATACCAACAAATAAAGCGCCGAAGCTGTTGTTGAAAGGTACAGGGAATTTAAAAGGTTCATCAGTTGGATATAAAAAAAT  >  USA300TCH1516_ALE/111372‑111652

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: ‑