Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,166,117 T→C 8.5% Y588C (TAC→TGC)  hrpA ← ATP‑dependent helicase HrpA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,166,1170TC 8.5% 128.6 / 3.5 47Y588C (TAC→TGC) hrpAATP‑dependent helicase HrpA
Reads supporting (aligned to +/- strand):  ref base T (24/19);  new base C (2/2);  total (26/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.76e-01

AGCAGCCCGCTGAGGATTGCCTTGTGCAGCTTCTGGTAATCGGTCGGTTCCTTGTTCACCGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCCACTGTGCGTGCGCCTGATCGGCGGC  >  NC_002947/5165988‑5166262
                                                                                                                                  |                                                                                                                                                 
agcagcCCTCTGAGGATTGCCTTGTGCAGCTTCTGGTAATCGGTCGGTTCCTTGTTCACCGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGCAGTTCCTGAACTACTTGCg                                                                                                                                <  2:217479/149‑1 (MQ=255)
    gcCCGCTGAGGATTGCCTTGTGCAGCTTCTGGTAATCGGTCGGTTCCTTGTTCACCGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGacac                                                                                                                            <  7:232409/149‑1 (MQ=255)
        gCTGAGGATTGCCTTGTGCAGCTTCTGGTAATCGGTCGGTTCCTTGTTCACCGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGt                                                                                                                        >  7:355647/1‑149 (MQ=255)
         cTGAGGATTGCCTTGTGCAGCTTCTGGTAATCGGTCGGTTCCTTGTTCACCGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGtt                                                                                                                       <  8:332676/149‑1 (MQ=255)
          tGAGGATTGCCTTGTGCAGCTTCTGGTAATCGGTCGGTTCCTTGTTCACCGTCAGCTGCAGGTCACGGCAAATCACCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTg                                                                                                                      >  8:243741/1‑149 (MQ=255)
               aTTGCCTTGTGCAGCTTCTGGTAATCGGTCGGTTCCTTGTTCACCGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAg                                                                                                                 >  6:275579/1‑149 (MQ=255)
                                         ggtcggtTCCTTGTTCACCGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCgtt                                                                                       >  3:125192/1‑149 (MQ=255)
                                         ggtcggtTCCTTGTTCACCGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCgtt                                                                                       >  8:202839/1‑149 (MQ=255)
                                                 ccTTGTTCACCGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTc                                                                                <  8:355647/148‑1 (MQ=255)
                                                     gTTCACCGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGaa                                                                             <  4:75736/147‑1 (MQ=255)
                                                     gTTCACCGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAgc                                                                           >  6:205115/1‑149 (MQ=255)
                                                        cACCGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAgccac                                                                        >  2:180651/1‑149 (MQ=255)
                                                         aCCGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGaa                                                                             >  6:146152/1‑143 (MQ=255)
                                                         aCCGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGaa                                                                             <  5:146152/143‑1 (MQ=255)
                                                          ccGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGCAgccacgc                                                                      >  6:247063/1‑149 (MQ=255)
                                                             tCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTCGGCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAgccacgcca                                                                    >  1:101829/1‑149 (MQ=255)
                                                               aGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAg                                                                 <  7:243741/149‑1 (MQ=255)
                                                                    cAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGa                                                            >  7:163315/1‑149 (MQ=255)
                                                                     aGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGAc                                                           <  7:202839/149‑1 (MQ=255)
                                                                       gTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACca                                                         >  6:352683/1‑149 (MQ=255)
                                                                        tCACGGCAAATGAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCTGGTACTGGTTGCGacac                                                                                                                            <  8:132951/81‑1 (MQ=255)
                                                                        tCACGGCAAATCACCGCCTACTGACGATGAGCATCGCGCCACTC‑CCGCAGCCGCAACTACTTCACCAACTCCTTGCGacac                                                                                                                            >  7:132951/1‑81 (MQ=255)
                                                                             gCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACcagcgcag                                                   <  2:101829/149‑1 (MQ=255)
                                                                               aaaTCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACcagcgcagc                                                  >  4:249811/1‑148 (MQ=255)
                                                                                     gcgcCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTcc                                           <  5:275579/149‑1 (MQ=255)
                                                                                           aCTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTcc                                     <  5:247063/149‑1 (MQ=255)
                                                                                               aCGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCAc                                   <  8:133497/147‑1 (MQ=255)
                                                                                               aCGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCAc                                   <  4:125192/147‑1 (MQ=255)
                                                                                                cGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTc                                <  5:205115/149‑1 (MQ=255)
                                                                                                       cATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCCAc                         >  5:78564/1‑149 (MQ=255)
                                                                                                       cATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCCAc                         >  7:52402/1‑149 (MQ=255)
                                                                                                             gcCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAgc                                                                           >  6:207171/1‑93 (MQ=255)
                                                                                                             gcCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAgc                                                                           <  5:207171/93‑1 (MQ=255)
                                                                                                                 cTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCTACTgtgcgtgc                >  1:312048/1‑148 (MQ=255)
                                                                                                                 cTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCCCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCCACTgtgcgtgc                <  2:312048/148‑1 (MQ=255)
                                                                                                                  tC‑GCGCAGCCGCAAGTAGTTCGGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCCACTGTGCGTgcgc              >  1:328218/1‑149 (MQ=255)
                                                                                                                          gtcGCAAGCAGTTCCTGAACTACTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCCACtgt                      <  6:306407/132‑1 (MQ=255)
                                                                                                                          gtcGCAAGCAGTTCCTGAACTACTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCCACtgt                      >  5:306407/3‑134 (MQ=255)
                                                                                                                            cGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCCACTGTGCGTGCGCCTGATcggc     >  6:25248/1‑149 (MQ=255)
                                                                                                                            cGCAAGCAGTTCCTGAACTACTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCCACTGTGCGTGCGCCTGATcggc     >  7:127989/1‑149 (MQ=255)
                                                                                                                             gCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCCACTGTGCGTGCGCCTGATcggcg    >  7:208200/1‑149 (MQ=255)
                                                                                                                             gCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCCACTGTGCGTGCGCCTGATcggcg    >  7:202766/1‑149 (MQ=255)
                                                                                                                             gCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCCACTGTGCGTGCGCCTGATcggcg    >  4:63419/1‑149 (MQ=255)
                                                                                                                              cAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTcc                           <  6:234157/125‑1 (MQ=255)
                                                                                                                              cAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTcc                           >  5:234157/1‑125 (MQ=255)
                                                                                                                               aaGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCCACTGTGCGTGCGCCTGATCggcggc  <  8:202766/149‑1 (MQ=255)
                                                                                                                               aaGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCCACTGTGCGTGCGCCTGATCggcggc  <  8:208200/149‑1 (MQ=255)
                                                                                                                                  |                                                                                                                                                 
AGCAGCCCGCTGAGGATTGCCTTGTGCAGCTTCTGGTAATCGGTCGGTTCCTTGTTCACCGTCAGCTGCAGGTCACGGCAAATCAGCGCCAACTGACGATGAGCATCGCGCCACTC‑GCGCAGCCGCAAGTAGTTCAGGAACTGCTTGCGACACCAGTTGCGCAGCGGGTTGGCGGTCAGCGCCTGGCGTTGTTCCTCGAAGCCACGCCACAGGTTGACCAGCGCAGCGAAGTCCGAGTCCACGTCCTTCCACTGTGCGTGCGCCTGATCGGCGGC  >  NC_002947/5165988‑5166262

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: ‑