Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 231,978 T→C 9.4% M48T (ATG→ACG)  USA300HOU_0209 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730231,9780TC 9.4% 102.3 / 3.7 43M48T (ATG→ACG) USA300HOU_0209hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (19/19);  new base C (2/2);  total (21/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.24e-01

GGATAATAGAAATATGATTAATCGTGTTTTTAGTCAAAAGATATTACATCAAATTGCAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTCTAGGACGACATTCTATTAATACAACTACTGCACTTTCTGAGATGCCCAT  >  CP000730/231838‑232107
                                                                                                                                            |                                                                                                                                 
aataaagaGAAATATGATTAATCGTGTTTTTAGTCAAAAGATATTACATCAAATTGCAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGAt                                                                                                                                   <  2:188021/134‑1 (MQ=255)
         aaaTATGATTAATCGTGTTTTTAGTCAAAAGATATTACATCAAATTGCAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCttt                                                                                                                          >  2:330113/1‑141 (MQ=255)
          aaTATGATTAATCGTGTTTTTAGTCAAAAGATATTACATCAAATTGCAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTta                                                                                                                         >  2:336999/1‑141 (MQ=255)
          aaTATGATTAATCGTGTTTTTAGTCAAAAGATATTACATCAAATTGCAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGACGAAATCTTta                                                                                                                         >  2:81222/1‑141 (MQ=255)
          aaTATGATTAATCGTGTTTTTAGTCAAAAGATATTACATCAAATTGCAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGACGAAATCTTta                                                                                                                         >  2:81465/1‑141 (MQ=255)
               gATTAATCGTGTTTTTAGTCAAAAGATATTACATCAAATTGCAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATaa                                                                                                                    >  1:176945/1‑141 (MQ=255)
                aTTAATCGTGTTTTTAGTCAAAAGATATTACATCAAATTGCAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAAc                                                                                                                   >  2:197432/1‑141 (MQ=255)
                  aaaTCGTGTAATTAAACAAAAGATATAACATCAAATTGCAATCAAAAATAAAAATGATGTTGTAAATGAGGCATATGATTTACATATACAAAGACCTAAAAACATCAATGTAATACAGAAGATGAAATCTTTATATAACTa                                                                                                                 <  2:256842/140‑1 (MQ=255)
                      cGTGTTTTTAGTCAAAAGATATTACATCAAATTGCAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCtt                                                                                                             <  2:321292/141‑1 (MQ=255)
                              tAGTCAAAAGATATTACATCAAATTGCAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTc                                                                                                     <  1:61418/141‑1 (MQ=255)
                                 tCAAAAGATATTACATCAAATTGCAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTa                                                                                                  >  1:322307/1‑141 (MQ=255)
                                  cAAAAGATATTACATCAAATTGCAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTAt                                                                                                 <  1:254447/141‑1 (MQ=255)
                                  cAAAAGATATTACATCAAATTGCAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTACCTTAAAAAGTCTTAt                                                                                                 >  2:252378/1‑141 (MQ=255)
                                          atTACATCAAATTGCAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGa                                                                                         >  2:65656/1‑141 (MQ=255)
                                                        cAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACaaaa                                                                           >  2:338595/1‑141 (MQ=255)
                                                              aaaaTAAAAGTGAGGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGCATATTTTTACAAAAACACaa                                                                     <  2:3562/141‑1 (MQ=255)
                                                                aaTAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATGTTTTTACAAAAACACAATa                                                                   <  1:229324/141‑1 (MQ=255)
                                                                aaTAAAAGGGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATa                                                                   <  1:149670/141‑1 (MQ=255)
                                                                   aaaaGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACtt                                                                <  1:383229/141‑1 (MQ=255)
                                                                   aaaaATGATGTTGTTGATGAGGCATATTATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACtt                                                                <  1:64878/141‑1 (MQ=255)
                                                                    aaaGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTta                                                               >  2:234166/1‑141 (MQ=255)
                                                                    aaaGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTta                                                               >  2:31118/1‑141 (MQ=255)
                                                                                ttgATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTc                                                   >  2:19280/1‑141 (MQ=255)
                                                                                ttgATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTc                                                   <  1:336999/141‑1 (MQ=255)
                                                                                ttgATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGACGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTc                                                   <  1:81222/141‑1 (MQ=255)
                                                                                ttgATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGACGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTc                                                   <  1:81465/141‑1 (MQ=255)
                                                                                ttgATGAGGCATATGATTTCTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTc                                                   >  2:228309/1‑141 (MQ=255)
                                                                                      gggCATATGATTTTTATATACAGGGACCTAAAAATAGCAATGTAATACAGAAGATGAAATCTTTATATAACTAGCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTCTAGgac                                             <  1:309289/140‑1 (MQ=255)
                                                                                                 ttttATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCATATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTCTAGGACGACATTCTAtt                                  >  2:284973/1‑141 (MQ=255)
                                                                                                   ttATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTCTAGGACGACATTCTATTaa                                >  2:379880/1‑141 (MQ=255)
                                                                                                    tatataCAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTCTAGGACGACATTCTATTAAt                               <  2:203586/141‑1 (MQ=255)
                                                                                                    tatataCAGGAACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTCTAGGACGACATTCTATTAAt                               <  2:317060/141‑1 (MQ=255)
                                                                                                     atataCAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCCTATCGTCACGAACATTTTTCCAAAAACACACTACTTACTCAACTCCTTCTACGACCACATCCTATAAATa                              >  2:325996/1‑141 (MQ=255)
                                                                                                      tataCAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACATAATACTTAATAAACTCCTTCTAGGACGACATTCtctaacttc                             >  2:72657/1‑133 (MQ=255)
                                                                                                       ataCAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTCTAGGACGACATTCTATTAATACa                            <  1:94812/141‑1 (MQ=255)
                                                                                                           aGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTCTAGGACGACATTCTATTAATACAacta                        <  1:60330/141‑1 (MQ=255)
                                                                                                            gggACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTCTAGGACGACATTCTATTAATACAactac                       >  2:243155/1‑141 (MQ=255)
                                                                                                                  tAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTTTAGGGCGCATTTCTATTAATACAACTAATGCACt                 >  1:138307/1‑141 (MQ=255)
                                                                                                                    aaaaTAACAGAGGAATACCGAAGAGGTATTCTTTATATAACTAGCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTCTAGGACGACATTCTATTAATACAACTACTGCACttt               <  1:179964/141‑1 (MQ=255)
                                                                                                                      aaTCTCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTCTAGGACGACATTCTATTAATACAACTACTGCACTGTCt             <  2:256488/141‑1 (MQ=255)
                                                                                                                      aaTATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTCTAGGACGACATTCTAATAATACAACTACTGCACCTTCt             >  2:37423/1‑141 (MQ=255)
                                                                                                                       atatCAATGTAATACAGAAGATCAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTCTAGGACGACATTCTATTAATACAACTACTGCACTTTCTg            <  2:9152/141‑1 (MQ=255)
                                                                                                                                gaaaaCAGAAGATGAAAGCTTTATATAACTATCTTAAAAAGTCTTATCGTAAGGAATAAAATTAAAAAAACACAATACTTAATAAACTCCTTCTAGGACGACATTCTATTAATACAACTACTGCACTTTCTGAGATGCCCa   <  2:141045/137‑1 (MQ=255)
                                                                                                                                 aaTAAAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTCTAGGACGACATTCTATTAATACAACTACTGCACTTTCTGAGATGCCCAt  <  1:369607/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                 
GGATAATAGAAATATGATTAATCGTGTTTTTAGTCAAAAGATATTACATCAAATTGCAATCAAAAATAAAAGTGATGTTGTTGATGAGGCATATGATTTTTATATACAGGGACCTAAAAATATCAATGTAATACAGAAGATGAAATCTTTATATAACTATCTTAAAAAGTCTTATCGTAACGAATATTTTTACAAAAACACAATACTTAATAAACTCCTTCTAGGACGACATTCTATTAATACAACTACTGCACTTTCTGAGATGCCCAT  >  CP000730/231838‑232107

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: ‑