Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,156,687 T→A 9.1% H35L (CAC→CTC)  PP_3659 ← transcriptional regulator, AraC family

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,156,6870TA 9.1% 118.7 / 3.7 44H35L (CAC→CTC) PP_3659transcriptional regulator, AraC family
Reads supporting (aligned to +/- strand):  ref base T (19/21);  new base A (2/2);  total (21/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.10e-01

TTGAAGCTACCTCTGCGAAGGGGATGACTGTCTGCCGCAAAAAACTCATCGTCGAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAACTCCATCTGGGGCTCCGTTGCTAACTCGATACCGAAGGCTG  >  NC_002947/4156540‑4156825
                                                                                                                                                   |                                                                                                                                          
ttGAAGCTACCTCTGCGAAGGGGATGACTGTCTGCCGCAAAAAACTCATCGTCGAGCAAATCGGCTAAAGAAATCCACAATCAGGAGCACGTACCAGCAGGAACCCTGGCATAGCGCTGGTCCAGCAGGAGAGGATCACTATGCGCGTg                                                                                                                                           >  8:250401/1‑149 (MQ=255)
  gAAGCTACCTCTGCGAAGGGGATGACTGTCTGCCGCAAAAAACTCATCGTCGAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGAAGGCGTGGATCAATATGCGCGTGGc                                                                                                                                         >  7:79326/1‑149 (MQ=255)
     gCTACCTCTGCGAAGGGGATGACTGTCTGCCGCAAAAAACTCATCGTCGAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGa                                                                                                                                      <  2:130377/149‑1 (MQ=255)
            ctGCGAAGGGGATGACTGTCTGCCGCAAAAAACTCATCGTCGAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGt                                                                                                                               >  4:113770/1‑149 (MQ=255)
               cGAAGGGGATGACTGTCTGCCGCAAAAAACTCATCGTCGAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTcgc                                                                                                                            <  4:149129/149‑1 (MQ=255)
                     ggATGACTGTCTGCCGCAAAAAACTCATCGTCGAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATc                                                                                                                      <  1:195067/149‑1 (MQ=255)
                     ggATGACTGTCTGCCGCAAAAAACTCATCGTCGAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATc                                                                                                                      <  3:113770/149‑1 (MQ=255)
                              tCTGCCGCAAAAAACTCATCGTCGAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCAc                                                                                                              <  6:296140/148‑1 (MQ=255)
                                     cAAAAAACTCATCGTCGAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCt                                                                                                      >  6:168373/1‑149 (MQ=255)
                                     cAAAAAACTCATCGTCGAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGAGGCTGAGCACAGTCGCGACa                                                                                                                        <  6:80066/131‑1 (MQ=255)
                                     cAAAAAACTCATCGTCGAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGAGGCTGAGCACAGTCGCGACa                                                                                                                        <  6:75601/131‑1 (MQ=255)
                                     cAAAAAACTCATCGTCGAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGAGGCTGAGCACAGTCGCGACa                                                                                                                        >  5:80066/1‑131 (MQ=255)
                                     cAAAAAACTCATCGTCGAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGAGGCTGAGCACAGTCGCGACa                                                                                                                        >  5:75601/1‑131 (MQ=255)
                                           aCTGATCGTCGAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGTTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTTGCTGAGCAGAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCt                                                                                                <  2:81123/149‑1 (MQ=255)
                                                  gtcgAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTg                                                                                         >  8:94152/1‑149 (MQ=255)
                                                       gCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTcc                                                                                    >  1:12693/1‑149 (MQ=255)
                                                          aaTCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCg                                                                                  >  3:144316/1‑148 (MQ=255)
                                                                   aTGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGc                                                                          <  7:167043/147‑1 (MQ=255)
                                                                           cacaATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACgt                                                                <  4:144316/149‑1 (MQ=255)
                                                                                tCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAg                                                                                           <  4:3229/117‑1 (MQ=255)
                                                                                tCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAg                                                                                           >  3:3229/1‑117 (MQ=255)
                                                                                        aCGTACCAGAAGGTTCCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTgg                                                   <  7:250401/149‑1 (MQ=255)
                                                                                         cGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGc                                                                          <  8:106034/125‑1 (MQ=255)
                                                                                         cGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGc                                                                          >  7:106034/1‑125 (MQ=255)
                                                                                             ccAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCttt                                                       >  4:90573/1‑140 (MQ=255)
                                                                                             ccAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCttt                                                       <  3:90573/140‑1 (MQ=255)
                                                                                                 cagGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAAc                                          <  2:12693/149‑1 (MQ=255)
                                                                                                 cagGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAAc                                          <  7:94152/149‑1 (MQ=255)
                                                                                                     cagccTGGCAAAGCGCTGGTCCAGCAGCCGTGGATCAATATGCGCGTGGCTGACCACACTCGCGACATCCACGCCACGTAGTTCTGCTCCTTGAAGCGCCTCCCGCACGAGGCTGATCGACGCGGTGCCTTTGTGGGCAGAAAACTCCa                                      <  6:8005/146‑1 (MQ=255)
                                                                                                        ccTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAACTCCATCt                                   >  1:49686/1‑149 (MQ=255)
                                                                                                          tGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAACTCCATCTgg                                 >  2:50194/1‑149 (MQ=255)
                                                                                                          tGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAACTCCATCTgg                                 >  5:257787/1‑149 (MQ=255)
                                                                                                             cATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAACTCCATCTGGGGc                              >  8:207278/1‑149 (MQ=255)
                                                                                                             cATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAACTCCATATgtgtc                              >  8:203518/1‑145 (MQ=255)
                                                                                                                aGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAACTCCATCTGGGGCTcc                           >  5:32529/1‑149 (MQ=255)
                                                                                                                           agcagGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACTTGGTGCCTTTGTGGGCAGAAAACTCCATCTGGGGCTCCGTTGCTAACTc                <  5:168373/149‑1 (MQ=255)
                                                                                                                                  gTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAACTCCATCTGGGGCTCCGTTGCTAACTCGATAcc          >  6:28207/1‑148 (MQ=255)
                                                                                                                                     gATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAACTCCATCTGGGGCTCCGt                         >  1:84531/1‑130 (MQ=255)
                                                                                                                                     gATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAACTCCATCTGGGGCTCCGt                         <  2:84531/130‑1 (MQ=255)
                                                                                                                                     gATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAACTCCATCTGGGGCTCCGTTGCTAACTCGATACCGAAg      >  2:89275/1‑149 (MQ=255)
                                                                                                                                      aTCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAACTCCATCTGGGGCTCCGTTGCTAACTCGATACCGAAgg     <  7:207278/149‑1 (MQ=255)
                                                                                                                                       tCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTCGGCAGAAAACTCCATCTGGGGCTCCGTTGCTAACTCGATACCGAAgg     <  7:203518/148‑1 (MQ=255)
                                                                                                                                         aaTATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAACTCCATCTGGGGCTCCGTTGCTAACTCGATACCGAAGGCTg  <  1:89275/149‑1 (MQ=255)
                                                                                                                                                gcgTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAgg                                                                           <  4:256112/69‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                          
TTGAAGCTACCTCTGCGAAGGGGATGACTGTCTGCCGCAAAAAACTCATCGTCGAGCAAATCCGCTAATGCAATCCACAATCTGGAGAACGTACCAGCAGGTACCCTGGCATAGCGCTGGTCCAGCAGGCGTGGATCAATATGCGCGTGGCTGAGCACAGTCGCGACATCCAGGCCACGTAGTTCTGCTCCTTGAAGTGCGTCCCGCACGAGGCTGATCGACGTGGTGCCTTTGTGGGCAGAAAACTCCATCTGGGGCTCCGTTGCTAACTCGATACCGAAGGCTG  >  NC_002947/4156540‑4156825

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑