Predicted mutation
evidence seq id position mutation freq annotation gene description
RA KT2440 484,863 C→T 8.2% R203H (CGT→CAT)  lptD ← LPS‑assembly protein LptD

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*KT2440484,8630CT 8.2% 151.9 / 3.7 49R203H (CGT→CAT) lptDLPS‑assembly protein LptD
Reads supporting (aligned to +/- strand):  ref base C (21/24);  new base T (2/2);  total (23/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.95e-01

ACGCTTGGCGTAAAGGGCACTGCCGCGGATGTGCGACTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGCATGCTGCCCTGGCGCATCACCACGTCACCGGCGAGGGTGGCGATCTGCTGCTCCTGCTG  >  KT2440/484733‑484996
                                                                                                                                  |                                                                                                                                     
aCGCTTGGCGTAAAGGGCACTGCCGCGGATGTGCGACTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGTGCCTCGTCACCGACCCCCAGGGAACCGGTGTCACGGAt                                                                                                                                   >  5:153777/1‑135 (MQ=255)
   cTTGGCGTAAAGGGCACTGCCGCGGATGTGCGACTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTg                                                                                                                               <  3:53790/136‑1 (MQ=255)
    ttGGCGTAAAGGGCACTGGCGCGGATGTGAGACTTGTGCATCACGTATTCGGCGTTGTCGAACTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTg                                                                                                                               <  2:327611/135‑1 (MQ=255)
    ttGGCGTAAAGGGCACTGCCGCGGATGTGCGACTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTg                                                                                                                               <  8:129829/135‑1 (MQ=255)
    ttGGCGTAAAGGGCACTGCCGCGGATGTGCGACTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTg                                                                                                                               <  8:6137/135‑1 (MQ=255)
    ttGGCGTAAAGGGCACTGCAGCGGATGTGCGACTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTg                                                                                                                               <  1:31373/135‑1 (MQ=255)
       gCGTAAAGGGCACTGCCGCGGATGTGCGACTTGTGCATCACGTATTCGGCGTTGTCGACCTGAGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGa                                                                                                                              <  7:265371/133‑1 (MQ=255)
                     gCCGCGGATGTGCGACTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCg                                                                                                             >  4:174135/1‑136 (MQ=255)
                     gCCGCGGATGTGCGACTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGGTGGCACGGCTCTTGACGTTGCCCTTGAGCTc                                                                                                              >  5:210759/1‑135 (MQ=255)
                      ccGCGGATGTGCGACTTGTGCAGCACGTATTCGGCGGTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGAGCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCg                                                                                                             <  1:144787/135‑1 (MQ=255)
                       cgcgGATGTGCGACTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCg                                                                                                             <  5:212192/134‑1 (MQ=255)
                       cgcgGATGTGCGACTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCCTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCg                                                                                                             <  8:117672/134‑1 (MQ=255)
                         cgGATGTGCGACTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCAc                                                                                                         >  4:5749/1‑136 (MQ=255)
                            aTGTGCGACTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCCCCGCCCACCCGGGACCCGGTGTCGCGGCTCTTGTCGTTGCCCTTGAGCTCGCCACGGt                                                                                                      >  3:34799/1‑136 (MQ=255)
                               tgCGACTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTTGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGttt                                                                                                    <  3:189434/135‑1 (MQ=255)
                                   aCTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCCCCAGGGAACCGTTGTCACGGATCTTGCCGTTGCCCTTGAGCTCGCCACGGTTTTCgg                                                                                                >  8:215909/1‑135 (MQ=255)
                                    cTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGc                                                                                               >  1:157651/1‑135 (MQ=255)
                                        tgCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTg                                                                                            <  2:234739/134‑1 (MQ=255)
                                         gCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTg                                                                                            >  7:111202/1‑133 (MQ=255)
                                           aTCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTa                                                                                         >  4:156091/1‑134 (MQ=255)
                                                gTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCt                                                                                             >  2:113153/1‑125 (MQ=255)
                                                gTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCt                                                                                             <  1:113153/125‑1 (MQ=255)
                                                  aTTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTg                                                                                            <  3:53132/124‑1 (MQ=255)
                                                  aTTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTg                                                                                            >  4:53132/1‑124 (MQ=255)
                                                     gggCGTTGTCGAGCTGGGCTTCGCGAGTGTCGAGCTGGATCTGGGCCTCGTCTCCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCGTGGTAGAGGTTGGCCt                                                                              <  4:175992/134‑1 (MQ=255)
                                                     cGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCt                                                                              >  1:191051/1‑135 (MQ=255)
                                                           tGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCgg                                                                        >  7:350501/1‑135 (MQ=255)
                                                              cGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCtt                                                                     >  1:314232/1‑135 (MQ=255)
                                                                     ggCTTCGCCTGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGG‑TTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGc                                                             <  7:99808/135‑1 (MQ=255)
                                                                     ggCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCATGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAgg                                                                                     <  7:284236/112‑1 (MQ=255)
                                                                     ggCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCATGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAgg                                                                                     >  8:289093/1‑112 (MQ=255)
                                                                     ggCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCATGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAgg                                                                                     <  7:289093/112‑1 (MQ=255)
                                                                     ggCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCATGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAgg                                                                                     >  8:284236/1‑112 (MQ=255)
                                                                     ggCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGc                                                             <  3:156091/136‑1 (MQ=255)
                                                                      gCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGc                                                             <  5:139426/135‑1 (MQ=255)
                                                                      gCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGc                                                             <  2:314232/135‑1 (MQ=255)
                                                                       cTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCCCGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGCAt                                                           >  4:78163/1‑136 (MQ=255)
                                                                              aGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGAATGCTGcc                                                     >  6:77469/1‑135 (MQ=255)
                                                                               gtgtCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGAATGCTGccc                                                    <  5:77469/135‑1 (MQ=255)
                                                                                           aTCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGCATGCTGCCCTGGCGCATca                                          <  8:67279/133‑1 (MQ=255)
                                                                                              tGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGCATGCTGCCCTGGCGCATCACCACGt                                    >  3:176545/1‑136 (MQ=255)
                                                                                              tGGGCCGCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGCATGCTGCCCTGGCGCATcaccac                                      <  4:231981/134‑1 (MQ=255)
                                                                                                 gCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGCATGCTGCCCTGGCGCATcaccac                                      <  2:29703/131‑1 (MQ=255)
                                                                                                  ccTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGCATGCTGCCCTGGCGCATCACCACGTCAcc                                <  4:93814/136‑1 (MQ=255)
                                                                                                   cTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCGGGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGCATGCTGCCCTGGCGCATCACCCCGTCTCCg                               >  3:245556/1‑136 (MQ=255)
                                                                                                         aCCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGCATGCTGCCCTGGCGCATCACCACGTCACCGGCGAgg                         >  3:107742/1‑136 (MQ=255)
                                                                                                                            ttGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGCATGCTGCCCTGGCGCATCACCACGTCCCCGGCGAGGGTGGCGATCTGCTGCTCct      >  3:71014/1‑136 (MQ=255)
                                                                                                                               tCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGc                                                             >  2:31401/1‑78 (MQ=255)
                                                                                                                               tCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGc                                                             <  1:31401/78‑1 (MQ=255)
                                                                                                                                  cGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGCATGCTGCCCTGGCGCATCACCACGTCACCGGCGAGGGTGGCGATCTGCTGCTCctgctg  >  8:47305/1‑134 (MQ=255)
                                                                                                                                  |                                                                                                                                     
ACGCTTGGCGTAAAGGGCACTGCCGCGGATGTGCGACTTGTGCATCACGTATTCGGCGTTGTCGACCTGGGCTTCGCCAGTGTCGAGCTGGATCTGGGCCTCGTCACCGACCACCAGGGAACCGTTGTCACGGATCTTGACGTTGCCCTTGAGCTCGCCACGGTTTTCGGCCTGGTAGAGGTTGGCCTCGTCGGCTTCGGCCTGCATGCTGCCCTGGCGCATCACCACGTCACCGGCGAGGGTGGCGATCTGCTGCTCCTGCTG  >  KT2440/484733‑484996

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑