Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 110,651 C→T 11.6% D170D (GAC→GAT)  USA300HOU_RS00515 → putative lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE110,6510CT11.6% 123.7 / 4.9 53D170D (GAC→GAT) USA300HOU_RS00515putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (15/30);  new base T (2/5);  total (18/35)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

AAAAGATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAG  >  USA300TCH1516_ALE/110511‑110787
                                                                                                                                            |                                                                                                                                        
aaaaGATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGAc                                                                                                                                          >  1:462260/1‑141 (MQ=255)
   aGATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGga                                                                                                                                       <  1:321724/141‑1 (MQ=255)
    aatatCCAGTTAAAATGAACAAAAATAAAAACATTACAACAAAAGAAATTAAAGATAAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTCCATCTTTGAAAAATTATAAAGACGgag                                                                                                                                      <  2:250185/140‑1 (MQ=17)
        tCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAAACGAAAACTTTAAGTTCTTTGATCAATATAGAGACTTTAAAAATTTGAAAAAATATAAAGACGGAGatat                                                                                                                                  >  2:379127/1‑141 (MQ=17)
           ggTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGAGACTTTAAAAATTTGAAAAATTATAAAAAAGGAGATATTTc                                                                                                                               >  2:412845/1‑141 (MQ=255)
               aaaaTGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCatat                                                                                                                           <  1:173352/141‑1 (MQ=255)
                 aaTGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACAGAGATATTTCATATaa                                                                                                                         >  2:413286/1‑141 (MQ=255)
                 aaTGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAACATGAAAAAATAAAAAAAGAAATCAAAAACTTTAAGTTCTTTGTTCAATATGGCTACTTTAAAAATTTGAAACATTATAAAGACTGAAATATTTAATATaa                                                                                                                         >  2:340059/1‑141 (MQ=17)
                    ggTCGAAAAAAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATcc                                                                                                                      <  1:329435/141‑1 (MQ=255)
                       cGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCaga                                                                                                                   <  2:290659/141‑1 (MQ=255)
                          taataaAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGt                                                                                                                >  1:304992/1‑141 (MQ=255)
                             taaAATAATTCCAACAAAAGAAAGTAAAGATGAAAAAATAAAAAAAGAAAGCGAAAACTTGAAGTTCTTTGTTCAATACGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGcc                                                                                                             <  1:445981/141‑1 (MQ=17)
                                 ataaTTCAAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGt                                                                                                         <  1:155913/138‑1 (MQ=255)
                                 aTCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGt                                                                                                         <  1:420244/141‑1 (MQ=255)
                                   cATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGATGCCTAGTTa                                                                                                       >  2:426045/1‑141 (MQ=255)
                                      tCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTc                                                                                                    >  1:199727/1‑141 (MQ=255)
                                        caacaaAAGAAATTAAAGAGGAAAAAATAAAAAAAGAAATCGAAAAATTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCgg                                                                                                  <  1:137162/141‑1 (MQ=255)
                                         aacaaAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGc                                                                                                 >  1:144244/1‑141 (MQ=255)
                                             aaaGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTaaa                                                                                             >  1:144364/1‑141 (MQ=255)
                                               aaaaaaTAAAGATAGAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                           <  2:258318/139‑1 (MQ=255)
                                               aGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                           <  2:68921/141‑1 (MQ=255)
                                               aGAAATTAAAGATGAAAAAATAAAAAAAGAAATAGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAata                                                                                           <  2:138077/141‑1 (MQ=255)
                                                   aTTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCaa                                                                                       <  1:244685/141‑1 (MQ=255)
                                                       aaGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTATATATCAATTaa                                                                                   >  2:384375/1‑141 (MQ=255)
                                                         gATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACt                                                                                 <  1:112601/141‑1 (MQ=255)
                                                           tGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTaa                                                                               <  1:255901/141‑1 (MQ=255)
                                                              aaaaagaaaaagAGAAGTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatga                                                                            <  2:219914/141‑1 (MQ=255)
                                                              aaaaaaaaaaaaaaaaaaCAAAAACTTTAAGTTAATTGTAAAAGAAGGCGACATTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatga                                                                            <  2:244916/141‑1 (MQ=17)
                                                              aaaaaaaaaaaaAGAAATCTAAAATTTTAAGTAATTGTTTGAATATAGCGCTTCCAAAAATTTTAAAAATTATAAATACGCAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatga                                                                            <  2:245035/141‑1 (MQ=17)
                                                               aaaaTAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTCAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAatgat                                                                           >  2:215726/1‑141 (MQ=255)
                                                                     aaaaaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                     >  2:220174/1‑141 (MQ=255)
                                                                     aaaaaaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATtat                                                                     >  1:289815/1‑141 (MQ=255)
                                                                         aaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATg                                                                 <  1:7020/141‑1 (MQ=255)
                                                                         aaGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATg                                                                 <  1:121819/141‑1 (MQ=255)
                                                                            aaaTCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTaa                                                              <  2:146554/141‑1 (MQ=255)
                                                                               tCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAAc                                                           >  1:173725/1‑141 (MQ=255)
                                                                                                  tGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatga                                        <  2:144244/141‑1 (MQ=255)
                                                                                                     tCAATATGTCGACTTACAAAATTTTAAAAATTATAAAGACGGAGATATGTCAGACAGCCCGGTCGAGCAGAGTTAGTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgatat                                     <  1:18684/141‑1 (MQ=17)
                                                                                                     tCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAgatatgatat                                     >  1:461744/1‑141 (MQ=255)
                                                                                                             gCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACcgacga                             <  1:428773/141‑1 (MQ=255)
                                                                                                              cGACGTAAAAAATTTGAAAAAGTAGAAAGACGGAGATATTTCATATAAGACAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAAGTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAg                            <  2:283973/141‑1 (MQ=17)
                                                                                                                 ttttAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTaa                         <  2:388307/140‑1 (MQ=11)
                                                                                                                    tAAAGATTTAATGAATTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGc                      <  1:208889/141‑1 (MQ=11)
                                                                                                                    tAAAAATTTGAAAAATAATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGTCGAGAAAAgg                      >  2:52936/1‑140 (MQ=255)
                                                                                                                     aaaaaTTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCt                     <  1:55163/141‑1 (MQ=255)
                                                                                                                          tttGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCaaa                <  2:60051/141‑1 (MQ=255)
                                                                                                                             aatgaaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGtt             <  1:480476/137‑1 (MQ=255)
                                                                                                                              aaaaaTTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTAGACTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTa            <  2:57363/141‑1 (MQ=255)
                                                                                                                                 aaTTATAAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTg         <  1:109560/141‑1 (MQ=255)
                                                                                                                                     ataAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaa     <  1:21278/141‑1 (MQ=255)
                                                                                                                                     ataAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGCTGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaa     <  1:266976/141‑1 (MQ=255)
                                                                                                                                      taAAGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaa    >  2:430333/1‑141 (MQ=255)
                                                                                                                                       aaaGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTaaaa   <  2:219220/141‑1 (MQ=255)
                                                                                                                                        aaGATGGAGATATATCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAACGTTATTGTTAAAAg  >  2:146377/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                        
AAAAGATATCCGGTTAAAATGGTCGATAATAAAATCATTCCAACAAAAGAAATTAAAGATGAAAAAATAAAAAAAGAAATCGAAAACTTTAAGTTCTTTGTTCAATATGGCGACTTTAAAAATTTGAAAAATTATAAAGACGGAGATATTTCATATAATCCAGAGGTGCCGAGTTATTCGGCTAAATATCAATTAACTAATGATGATTATAATGTAAAACAATTACGCAAAAGATATGATATACCGACGAGTAAAGCTCCAAAGTTATTGTTAAAAG  >  USA300TCH1516_ALE/110511‑110787

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: ‑