Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,987,440 T→C 9.1% L232S (TTG→TCG) ‡ PP_1778 → lipopolysaccharide ABC transporter permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,987,4400TC 9.1% 121.1 / 3.2 44L232S (TTG→TCG) ‡PP_1778lipopolysaccharide ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base T (20/20);  new base C (2/2);  total (22/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

GTGCTGCAGGTGTTGTTCTGGTTTACCCCAATCGTTTACATGGTCAATGTGATACCTGAACACCTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTACTATGAGCCTTTTGAGTGTCAGTGATGTGGGCAAAGCCTACAAAACGTACCG  >  NC_002947/1987292‑1987586
                                                                                                                                                    |                                                                                                                                                  
gTGCTGCAGGTGTTGTTCTGGTTTACCCCAATCGTTTACATGGTCAATGTGATACCTGAACACCTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGAttt                                                                                                                                                    <  6:128532/149‑1 (MQ=255)
          tgttgtTCTGGTTTACCCCAATCGTTTACATGGTCAATGTGATACCTGAACACCTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCg                                                                                                                                          <  2:73745/149‑1 (MQ=255)
               ttCTGGTTTACCCCAATCGTTTACATGGTCAATGTGATACCTGAACACCTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGt                                                                                                                                     >  1:215375/1‑149 (MQ=255)
               ttCTGGTTTACCCCAATCGTTTACATGGTCAATGTGATACCTGAACACCTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGATTGt                                                                                                                                     >  6:215763/1‑149 (MQ=255)
                  tGGTTTACCCCAATCGTTTACATGGTCAATGTGATACCTGAACACCTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGATTGTCAt                                                                                                                                  <  5:215763/149‑1 (MQ=255)
                         ccccAATCGTTTACATGGTCAATGTGATACCTGAACACCTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCgg                                                                                                                            >  1:229203/1‑148 (MQ=255)
                         ccccAATCGTTTACATGGTCAATGTGATACCTGAACACCTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCgg                                                                                                                            <  1:46539/148‑1 (MQ=255)
                             aaTCGTTTACATGGTCAATGTGATACCTGAACACCTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGAttt                                                                                                                       >  5:318898/1‑149 (MQ=255)
                                 gTTTACATGGTCAATGTGATACCTGAACACCTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCtt                                                                                                                   <  2:229203/149‑1 (MQ=255)
                                   ttACATGGTCAATGTGATACCTGAACACCTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGACTCAAATCAGGCGCttta                                                                                                                                     >  6:253223/1‑127 (MQ=255)
                                   ttACATGGTCAATGTGATACCTGAACACCTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGACTCAAATCAGGCGCttta                                                                                                                                     <  5:253223/129‑3 (MQ=255)
                                          gTCAATGTGATACCTGAACACCTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCtgtt                                                                                                          <  8:252272/149‑1 (MQ=255)
                                                            cacCTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGcctgttcct                                                                                        <  2:215375/149‑1 (MQ=255)
                                                               cTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGcctgttcctgtt                                                                                     >  1:91434/1‑149 (MQ=255)
                                                                     gCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTtcgtcg                                                                               >  3:175542/1‑149 (MQ=255)
                                                                      ccACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCgg                                                                              >  5:73293/1‑149 (MQ=255)
                                                                       cACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGt                                                                             >  6:177024/1‑149 (MQ=255)
                                                                       cACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGt                                                                             <  4:175542/149‑1 (MQ=255)
                                                                                        ccATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAAtggtg                                                            <  6:73293/149‑1 (MQ=255)
                                                                                         cATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAAtggtgg                                                           <  1:250627/149‑1 (MQ=255)
                                                                                            gTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATg                                                        >  1:83401/1‑149 (MQ=255)
                                                                                               tCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTAc                                                     <  3:103308/149‑1 (MQ=255)
                                                                                                 ccATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAGGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTACTa                                                   >  7:250178/1‑149 (MQ=255)
                                                                                                         aCTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGcctgttcctgt                                                                                      >  6:238913/1‑106 (MQ=255)
                                                                                                         aCTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGcctgttcctgt                                                                                      <  5:238913/106‑1 (MQ=255)
                                                                                                           tGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTACTATGAGCCtttt                                         <  2:83401/149‑1 (MQ=255)
                                                                                                                aTCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAAtggtg                                                            <  4:207997/125‑1 (MQ=255)
                                                                                                                aTCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAAtggtg                                                            >  3:207997/1‑125 (MQ=255)
                                                                                                                          aCTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTACTATGAGCCTTTTGAGTGTCAGTGAtgt                          >  4:159132/1‑149 (MQ=255)
                                                                                                                           cTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTACTATGAGCCTTTTGAGTGTCAGTGAtgtg                         <  2:91434/149‑1 (MQ=255)
                                                                                                                            tCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAAtg                                                               <  3:73339/110‑1 (MQ=255)
                                                                                                                            tCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAAtg                                                               >  4:73339/1‑110 (MQ=255)
                                                                                                                            tCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTACt                                                    >  8:109023/1‑121 (MQ=255)
                                                                                                                              cTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTg                                                                                                                 >  8:199562/1‑58 (MQ=255)
                                                                                                                              cTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTg                                                                                                                 <  7:199562/58‑1 (MQ=255)
                                                                                                                                 tACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTACTATGAg                                               >  1:99438/1‑121 (MQ=255)
                                                                                                                                 tACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTACTATGAg                                               <  2:99438/121‑1 (MQ=255)
                                                                                                                                      tAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTACTATGAGCCTTTTGAGTGTCAGTGATGTGGGCAAAGCCTa              >  4:42272/1‑149 (MQ=255)
                                                                                                                                         accgcCTGACTCAAATCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTACTATGAGCCTTTTGAGTGTCAGTGATGTggg                       <  6:40374/135‑1 (MQ=255)
                                                                                                                                         accgcCTGACTCAAATCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTACTATGAGCCTTTTGAGTGTCAGTGATGTggg                       >  5:40374/3‑137 (MQ=255)
                                                                                                                                              cTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTACTATGAGCCTTTTGAGTGTCAGTGATGTGGGCAAAGCCTACAAAACGt      <  3:42272/149‑1 (MQ=255)
                                                                                                                                                 aTTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCtgtt                                                                                                          >  6:249039/1‑46 (MQ=255)
                                                                                                                                                 aTTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCtgtt                                                                                                          <  5:249039/46‑1 (MQ=255)
                                                                                                                                                 aTTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTACTATGAGCCTTTTGa                                       <  6:13999/113‑1 (MQ=255)
                                                                                                                                                 aTTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCATGAAATGGTGGATGTACTATGAGCCTTTTGa                                       >  5:13999/1‑113 (MQ=255)
                                                                                                                                                  tttGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTACTATGAGCCTTTTGAGTGTCAGTGATGTGGGCAAAGCCTACAAAACGTACCg  >  5:307024/1‑149 (MQ=255)
                                                                                                                                                    |                                                                                                                                                  
GTGCTGCAGGTGTTGTTCTGGTTTACCCCAATCGTTTACATGGTCAATGTGATACCTGAACACCTTCGGGCCACCCTTAGTTTTAACCCCATGTATCCCATTGTTACTGCCTATCACGACGTACTCCTGTACGCTAAAGCGCCTGATTTGAGTCAGGCGGTTGTCATGACCGGGATTTCCTTTGGTCTGTTGTTGCTTGGCCTGTTCCTGTTTCGTCGGTCTGTGCCTGAAATGGTGGATGTACTATGAGCCTTTTGAGTGTCAGTGATGTGGGCAAAGCCTACAAAACGTACCG  >  NC_002947/1987292‑1987586

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑