Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE110,8050GA58.9% 24.4 / 57.7 56G222S (GGC→AGC) USA300HOU_RS00515putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base G (12/11);  new base A (19/14);  total (31/25)
Fisher's exact test for biased strand distribution p-value = 7.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.39e-01
Rejected as consensus: Frequency below/above cutoff threshold.

ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATAAAAAAAGCGGAGATGTATAATCATGGCTCAATCAGAATATGAAATCAATCC  >  USA300TCH1516_ALE/110668‑110943
                                                                                                                                         |                                                                                                                                          
aTCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATATAAAAAGCt                                                                                                                                         >  2:38737/1‑141 (MQ=255)
      agGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAg                                                                                                                                   >  2:34958/1‑141 (MQ=255)
         tGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCATAGTTGTTGTGGAAAGGATCAGGTAATCTAAAAGGCTCATCAGGTg                                                                                                                                >  1:145250/1‑141 (MQ=17)
          gCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTgg                                                                                                                               >  1:106267/1‑141 (MQ=255)
          gCCGAGTTATGCGGCTAAATATGAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTgg                                                                                                                               <  2:256470/141‑1 (MQ=255)
             gAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCAAAAGTTATTGTTAGCGGCTGCAGTTAATGTAAAAAGCTCATCAGTTGGata                                                                                                                            >  1:39210/1‑141 (MQ=18)
                 tATTCGGCTAAATATCAATTAACTAATGATGTTTTTACTGCAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATaaa                                                                                                                        <  1:120155/141‑1 (MQ=255)
                   ttCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGTGAATTTAAAAGGCTCATCAGTTGGATATAAAGa                                                                                                                      <  2:20540/141‑1 (MQ=255)
                   ttCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATAAAGa                                                                                                                      <  1:62665/141‑1 (MQ=255)
                    tCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATAAAGat                                                                                                                     >  1:20256/1‑141 (MQ=255)
                    tCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGAAAAAGATATGATATACAGACGCGTACAGCTACAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATAAAGat                                                                                                                     >  1:261595/1‑141 (MQ=18)
                     cGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGata                                                                                                                    <  1:151455/141‑1 (MQ=255)
                       gCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAACTACGCGAGACGGATTATATCACGCCCAGAAAATCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTGAAAAAGCTCATCAGTTGGATATAAAGATAtt                                                                                                                  <  1:251016/141‑1 (MQ=21)
                        cTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTg                                                                                                                 <  2:144167/141‑1 (MQ=255)
                         gaaaTATCAATGAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGa                                                                                                                <  1:98923/140‑1 (MQ=255)
                           aaaatCAATTAAATAATGAAGATTATAATTTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAAt                                                                                                              <  2:204503/138‑1 (MQ=21)
                            atatCAATTAACTAATGATGATTATAATGTAAAACAATACAGCACATGGTATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATAAAGATATTGAAtt                                                                                                             <  1:120659/141‑1 (MQ=21)
                               tCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATAAAGATATTGAATTTAc                                                                                                          >  2:119007/1‑141 (MQ=255)
                               tCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTAc                                                                                                          >  1:256347/1‑141 (MQ=255)
                                    tAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTg                                                                                                     >  1:137418/1‑141 (MQ=255)
                                      aCTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAATCGGTTCAACCAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTa                                                                                                   >  1:53764/1‑141 (MQ=21)
                                             atgatTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGaaaa                                                                                            <  1:3229/141‑1 (MQ=255)
                                             atgatTATAATGTAAAAAAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGaaaa                                                                                            <  2:21727/141‑1 (MQ=255)
                                             ataatTATAATGTAAAACAACTGCAAAAAATATATGATAGAACGACGAGTAAAGCTCCAAAGTTAATGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGAATATAAAGATAATGAATTTACGTTTGTAGAGaaaa                                                                                            <  2:87820/138‑1 (MQ=18)
                                              ttatTATAATGTAAAACAATTACGAAAAATATATAATATACAGACGAGTAAAGCTACAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGaaaaa                                                                                           <  1:76818/139‑1 (MQ=18)
                                              tgatTATAATGTAAAACAATTACGCAAAAGATATGATATAGCGACGAGTAAAGCTCAAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGaaaaa                                                                                           <  2:32866/141‑1 (MQ=255)
                                              tgatTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGaaaaa                                                                                           <  1:239403/141‑1 (MQ=255)
                                                    taATGTAAAACAATTACGCGAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAACAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTATGTAGAGAAAAActaaga                                                                                     >  2:230003/1‑141 (MQ=37)
                                                         tAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAATGTTCAGGGAATTTAAAAAGCCCATCAGTTGAATATAAAGATATTGAATTTACTTTTGTATAGAAAACAGAAGacaact                                                                                >  2:28948/1‑139 (MQ=255)
                                                         tAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAata                                                                                >  1:33152/1‑141 (MQ=255)
                                                         tAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAata                                                                                <  1:34958/141‑1 (MQ=255)
                                                         tAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAata                                                                                >  1:260937/1‑141 (MQ=255)
                                                           aaaCAATTACGTAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGAATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAatata                                                                              <  2:52496/141‑1 (MQ=255)
                                                                   aCGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAACAAGAAGAAAATATATACTTTAg                                                                      >  2:151816/1‑141 (MQ=255)
                                                                    cGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGATATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGt                                                                     >  2:107838/1‑141 (MQ=255)
                                                                          aGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTGAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTATAGAAAAAAGACGCAAATCGATACTTCAgaaataaa                                                               >  2:169097/1‑134 (MQ=18)
                                                                              atgatatATTGACGACTAAAGCTCCAAAGTTATTGTTAAAAGTTTCAGGGCATTTAATAAGCTCGTTAGTTGTATATAAAAATAATGCATTTACGATTCTCGATAAAAAAGAAGCAAATCTATACTTTAGTTATAGCttcc                                                           >  2:43619/1‑139 (MQ=255)
                                                                                gatatACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGAt                                                         >  2:1968/1‑141 (MQ=255)
                                                                                 atatACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGAtt                                                        >  1:128695/1‑141 (MQ=255)
                                                                                     aCCGACGAGTAAAGCTCCAAAGTTATTATGAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGATGGATATAAAGCTATTGAATTTACGTTTGTAGAGAAAAAATAAAAAAATATATACTATAGTGATACCTTAGATTATaa                                                    >  2:246450/1‑141 (MQ=21)
                                                                                        gacgaGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATaaaaa                                                 <  1:185931/141‑1 (MQ=255)
                                                                                         acgaGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATaaaaaa                                                <  1:163253/141‑1 (MQ=255)
                                                                                             gTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATAAAAAAAGCg                                            >  1:24979/1‑141 (MQ=255)
                                                                                             gTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATAAAAAAAGCg                                            <  1:84004/141‑1 (MQ=255)
                                                                                             gTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAAATATTAAATTTACGTTTGTAGAGAAAAAAGAAGAAAACATATACTTTAATGCTAGCTTAGATTATAAAAAAAGCg                                            <  1:135521/141‑1 (MQ=21)
                                                                                                aaGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATAAAAAAAGCGgag                                         >  1:255241/1‑141 (MQ=255)
                                                                                                aaGCTCCAAAGATATTGTTAAAAGGTTCAGGGAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATAAAAAAAgaggag                                         >  2:192797/1‑141 (MQ=255)
                                                                                                      cAAATTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATAAAAAAAGCGGAGATGtat                                   <  1:1925/141‑1 (MQ=255)
                                                                                                                tttAAAAGATTTACGGCATTTAAAAAGCTCATCAGTAGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATAAAAAAAGCGGAGATGTATAATCATGGCt                         <  2:57871/140‑1 (MQ=25)
                                                                                                                        gtaaaaagAATTAAAAAAGCTAATAAGTTGGATATAAAAATATTGAATTTACGTATGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGATTAAATTATAAAAAAAGCGGAGATGTATAATCATGGCTCAATCAGa                 <  2:39210/134‑1 (MQ=37)
                                                                                                                            aGGGAATTTAAAAGGCTCATCAGTTGGATAAAGCCAGTATATATTTGCGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATAGAAAAAGCGGAGCTGTATAATCATGGATCAATCAGAataa             >  2:61609/1‑140 (MQ=25)
                                                                                                                             gggAATTTAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATAAAAAAAGCGGAGATGTATAATCATGGCTCAATCAGAATATg            >  1:136383/1‑141 (MQ=255)
                                                                                                                              ggAATTTAAAAGGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATAAAAAAAGCGGAGATGTATAATCATGGCTCAATCAGAATATGa           >  1:186498/1‑141 (MQ=255)
                                                                                                                                  tttAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATAAAAAAAGCGGAGATGTATAATCATGGCTCAATCAGAATATGAaatc       >  1:216206/1‑141 (MQ=255)
                                                                                                                                  tttAAAAAGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATAAAAAAAGCGGAGATGTATAATCATGGCTCAATCAGAATATGAaatc       >  1:198877/1‑141 (MQ=255)
                                                                                                                                       aaGGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATAAAAAAAGCGGAGACGTATAATCATGCGTCAATCAGAATATGAAAACAATcc  >  2:126115/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                          
ATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAGGTTCAGGGAATTTAAAAGGCTCATCAGTTGGATATAAAGATATTGAATTTACGTTTGTAGAGAAAAAAGAAGAAAATATATACTTTAGTGATAGCTTAGATTATAAAAAAAGCGGAGATGTATAATCATGGCTCAATCAGAATATGAAATCAATCC  >  USA300TCH1516_ALE/110668‑110943

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: ‑